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= psy14049
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 116 bits (290), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 51/84 (60%), Positives = 65/84 (77%)
Query: 1 MSTVCFRYKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLA 60
++ R + GQ +L EF+G EPSKKRKRRTSFTPQA+E LNA+FE+N P+G EIT A
Sbjct: 68 LNEAELRNQEGQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXA 127
Query: 61 HQLGYEREVIRIWFCNKRQALKNT 84
+L Y+REV+R+WF N+RQ LKNT
Sbjct: 128 KELNYDREVVRVWFSNRRQTLKNT 151
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 62.0 bits (149), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 38/55 (69%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
+KRKRRT+ + A + L HF ++ PS EI +A +L E+EV+R+WFCN+RQ
Sbjct: 86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
>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 = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 36/59 (61%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S++RK+RTS L F N P+ EIT +A QL E+EVIR+WFCN+RQ K
Sbjct: 94 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>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 = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 36/59 (61%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S++RK+RTS L F N P+ EIT +A QL E+EVIR+WFCN+RQ K
Sbjct: 101 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>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 = 58.9 bits (141), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 36/59 (61%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S++RK+RTS L F N P+ EIT +A QL E+EVIR+WFCN+RQ K
Sbjct: 102 SERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 58.5 bits (140), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 29/67 (43%), Positives = 37/67 (55%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
+KRK+RTS L +HF + PS EIT LA L E+EV+R+WFCN+RQ K
Sbjct: 98 RKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRM 157
Query: 85 VRMMSKG 91
G
Sbjct: 158 TPAAGAG 164
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 35/58 (60%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
++RK+RTS L F N P+ EIT +A QL E+EVIR+WFCN+RQ K
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>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 = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 35/59 (59%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S++RK+RTS L F N P+ EIT +A QL E+EVIR+WF N+RQ K
Sbjct: 98 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 35/59 (59%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S++RK+RTS L F N P+ +IT +A QL E+EVIR+WF N+RQ K
Sbjct: 99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 33/57 (57%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+RK+RTS L F N P+ EI +A QL E+EVIR+WFCN+RQ K
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 38/59 (64%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
++++RTS + L F + PS +IT +A+QLG E++V+R+WFCN+RQ K +
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 36/54 (66%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
++++RTS + L F ++ PS +IT +A+QLG E++V+R+WF N+RQ
Sbjct: 96 RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQ 149
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 38/57 (66%)
Query: 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
EP + ++ RT+ TP+ LE+L + +++P+ + +AH++G ++ V+++WF N R
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
R+ RT+FT +E+L F N +P + LA +L E + I+IWF N+R LK + R
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%)
Query: 10 SGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREV 69
S +N + + P KK+K RT F+ L +LN F+R + S ++ L++ L +
Sbjct: 6 SAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQ 65
Query: 70 IRIWFCNKR 78
++ WF N+R
Sbjct: 66 VKTWFQNQR 74
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 31/58 (53%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
K R+RRT+FT + L L F + S TE + +AH L ++IWF N+R K
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+R++RT FT Q L+ L A F+RN +P + +A +R+WF N+R
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 25/50 (50%)
Query: 34 TPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
TP+ L +L + F R PS E LA + G R I WF + R A KN
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+R++RT FT Q L+ L A F+RN +P + +A +R+WF N+R
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S ++ RTSFT + +E L FER +P LA ++ I++WF N+R
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L L F N + + L+ +LG I+IWF NKR +K +
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S RK RT ++ L L F++ + + E LA LG + ++IWF NKR
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 80 ALKNT 84
+K +
Sbjct: 61 KIKKS 65
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
K+R+ RT+F+ L+ L FER +P LA + I++WF N+R L+
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
K+R+ RT+FT LE L F R +P LA ++G I++WF N+R
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L L F N + + L+ +LG I+IWF NKR +K +
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L L F N + + L+ +LG I+IWF NKR +K +
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85
RT+F+ + L L F N + + L+ +LG I+IWF NKR +K +
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 60
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+R+ RT+FT + LE L FER +P LA + +++WF N+R
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRR 54
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 27 RKRRTSFTPQALELLNAHFER---NTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R++R +F+ QA E+LN +F N +PS LA + G + WF NKR K
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
Query: 84 TV 85
+
Sbjct: 62 NI 63
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 31/65 (47%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G + K R+ RT FT L L FE+ + S + LA LG + ++ W+ N+R
Sbjct: 11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRM 70
Query: 80 ALKNT 84
K +
Sbjct: 71 KWKKS 75
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 27 RKRRTSFTPQALELLNAHFER---NTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R++R +F QA E+LN +F N +PS LA + G + WF NKR K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 84 TV 85
+
Sbjct: 62 NI 63
>pdb|2E19|A Chain A, Solution Structure Of The Homeobox Domain From Human
Nil-2- A Zinc Finger Protein, Transcription Factor 8
Length = 64
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
L LL A++ N PS E++ +A + +V++ WF K QA + +V+
Sbjct: 15 LSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWF-EKMQAGQISVQ 62
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S R+ RT FT + LE L F+ +P LA ++ E + +WF N+R
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 27 RKRRTSFTPQALELLNAHFER---NTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R++R +F QA E+LN +F N +PS LA + G + WF NKR K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 84 TV 85
+
Sbjct: 62 NI 63
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 27 RKRRTSFTPQALELLNAHFER---NTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R++R +F QA E+LN +F N +PS LA + G + WF NKR K
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
Query: 84 TV 85
+
Sbjct: 63 NI 64
>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 = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 28 KRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
K ++S +PQA L F R + E +A + G +R+WF NKR
Sbjct: 7 KGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
KKR+ RT+FT LE L F++ +P LA + +++WF N+R
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 28 KRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
K ++S +PQA L F R + E +A + G +R+WF NKR
Sbjct: 7 KGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>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 = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L L F N + + L+ +LG I+IWF N+R +K +
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.9 bits (76), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
++S +PQA L F R + E +A + G +R+WF NKR
Sbjct: 1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 49
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
RT+F+ + L L F N + + L+ +LG I+IWF NKR
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKR 51
>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 = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L L F N + + L+ +LG I+IWF N R +K +
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
RT+FT LE L F R +P LA ++G I++WF N+R
Sbjct: 3 RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 51
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S R+ RT+FT L++L A F + +P +A ++ +++WF N+R
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRR 59
>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 = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
R+ RT+FT L L F + + S LA QL I++WF N+R
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>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 = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 27/56 (48%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
P K++K RTSFT + L F + + + E LA L ++ WF N+R
Sbjct: 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 32.3 bits (72), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
RT+F+ + L F N + + L+ +LG I+IWF NKR ++ +
Sbjct: 7 RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.3 bits (72), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
R+ RT+FT + L HF + + + + L+ +L ++IWF N+R
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>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 = 31.6 bits (70), Expect = 0.12, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 22/49 (44%)
Query: 34 TPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+PQA L F R + E +A + G +R+WF NKR K
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
P+KKRKRR FT L F + + S E LA + ++IWF N R
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
>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 = 30.8 bits (68), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 19/49 (38%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
RT + L L + N P L G VIR+WF NKR
Sbjct: 7 RTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G ++R R+T Q LEL F N + + +AH L I+IWF N+R
Sbjct: 15 GTNGLRRRGRQTYTRYQTLEL-EKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73
Query: 80 ALKNTV 85
LK +
Sbjct: 74 KLKKEI 79
>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 = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 30/62 (48%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
S +++ RT+F+ + L L F N + + L+ +LG ++ WF N R +K
Sbjct: 2 SDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
Query: 84 TV 85
+
Sbjct: 62 ST 63
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+FT LE L F R +P LA ++G I++WF N+R
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 51
>pdb|2DA4|A Chain A, Solution Structure Of The Homeobox Domain Of The
Hypothetical Protein, Dkfzp686k21156
Length = 80
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGT----EITTLAHQLGYEREVIRIWFCNKRQ 79
RT F+ + L L +++ G+ +I +A +L + E++R W N+R+
Sbjct: 12 RTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRR 65
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 29.3 bits (64), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+K R FT L+A F+ N PS T++ QLG E + +F N R
Sbjct: 96 KKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 26/60 (43%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
P+KKRKRR FT L F + + S E L + ++IWF N R K
Sbjct: 9 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTK 68
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
+K R FT L+A F+ N PS T++ QLG E + +F N R+
Sbjct: 98 KKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARR 150
>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 = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
K+K RT F+ L L F++ + S ++ L+ L + ++ WF N+R
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQR 55
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 28.9 bits (63), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
RK RT FT L L F + + S E + L ++IWF N+R
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+KR R+T Q LEL F N + + +AH L I+IWF N+R K
Sbjct: 2 ERKRGRQTYTRYQTLEL-EKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 27 RKRRTSFTP-QALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+++RTS+T Q LEL F N + + +AH L I+IWF N+R K
Sbjct: 29 KRQRTSYTRYQTLEL-EKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 36 QALELLNAHFER---NTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
QA E+LN +F N +PS LA + G + WF NKR
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 58
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+KR R+T Q LEL F N + + +AH L I+IWF N+R K
Sbjct: 2 RKRGRQTYTRYQTLEL-EKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 25/57 (43%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
RT+FT + L L F N + S +A L ++IWF N+R K R
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
F ++ +L + N +PS E LA G + WF N+RQ
Sbjct: 501 FKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQ 547
>pdb|2LFB|A Chain A, Homeodomain From Rat Liver Lfb1HNF1 TRANSCRIPTION
FACTOR, Nmr, 20 Structures
Length = 100
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 21 MEPSKK-RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQ 62
++P+KK R+ R + P + ++L +ER +PS E TL +
Sbjct: 4 IDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 46
>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 = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+RK R F+ + L F++ + S E LA L ++IWF N+R
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|1LFB|A Chain A, The X-Ray Structure Of An Atypical Homeodomain Present
In The Rat Liver Transcription Factor Lfb1(Slash)hnf1
And Implications For Dna Binding
Length = 99
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 21 MEPSKK-RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQ 62
++P+KK R+ R + P + ++L +ER +PS E TL +
Sbjct: 3 IDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 45
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 44 HFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
F N + + L+ +LG I+IWF NKR +K +
Sbjct: 4 EFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>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 = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+KR R+T Q LEL F N + + +AH L I+IWF N+R K
Sbjct: 2 RKRGRQTYTRYQTLEL-EKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 32 SFTPQALELLNAHFER-NTHPSGTEITTLAHQLGYEREVIRIWF 74
+ T +E+L +F + N HP T + +A + G E + WF
Sbjct: 7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWF 50
>pdb|2B8N|A Chain A, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
(tm1585) From Thermotoga Maritima At 2.70 A Resolution
pdb|2B8N|B Chain B, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
(tm1585) From Thermotoga Maritima At 2.70 A Resolution
Length = 429
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 17 EFIGMEPSKKRKRRT-SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWF- 74
E G+E S+ KR TP+ L + H N E +LA + G+ E+I
Sbjct: 230 EKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLD 289
Query: 75 CNKRQA 80
C R+A
Sbjct: 290 CEAREA 295
>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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 23/53 (43%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
RT++T L L F N + S LA L I+IWF N+R K
Sbjct: 7 RTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 34 TPQALELLNAHFER-NTHPSGTEITTLAHQLGYEREVIRIWF 74
T +E+L +F + N HP T + +A + G E + WF
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWF 51
>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 = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 10 SGQNHLTEF-IGME-PSKK-RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQ 62
+GQ L E G E P+KK R+ R + P + ++L +ER +PS E TL +
Sbjct: 96 AGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 151
>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 = 25.4 bits (54), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
KR R+T Q LEL F N + + +A+ L I+IWF N+R
Sbjct: 4 KRTRQTYTRYQTLEL-EKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR 55
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 27 RKRRTSFTP-QALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
RK+R +T Q LEL F N + + +A L ++IWF N+R +K
Sbjct: 2 RKKRCPYTKYQTLEL-EKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
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
0.321 0.131 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,513,965
Number of Sequences: 62578
Number of extensions: 82494
Number of successful extensions: 226
Number of sequences better than 100.0: 83
Number of HSP's better than 100.0 without gapping: 70
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 156
Number of HSP's gapped (non-prelim): 83
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)