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= 001086
(1159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.1 bits (87), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 28/38 (73%)
Query: 18 YSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
+ ++KY + +M+ L++ L+L+YKQV+TWF +R + K
Sbjct: 22 FQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 37.7 bits (86), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 26/38 (68%)
Query: 18 YSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
+ +KY + +M+ L+ L+L+YKQV+TWF +R + K
Sbjct: 41 FQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 37.4 bits (85), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 23 YPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53
YPT+ E + +AA +LT QV WFI RRR
Sbjct: 34 YPTEDEKKQIAAQTNLTLLQVNNWFINARRR 64
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 37.0 bits (84), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 14 LLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
L ++Y+ YP+ E LA A LT QV WF +R+RD+
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 36.6 bits (83), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 25/39 (64%)
Query: 17 FYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
F S KYP + ++GL+ LD + ++++ WF +R +DK
Sbjct: 27 FVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 33.9 bits (76), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRR-RDKGDNGI 60
+ K KT Q K L + + +PT++E++ L L+ +++ +WF E+R+ RD + +
Sbjct: 16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV 75
Query: 61 V 61
+
Sbjct: 76 L 76
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 33.9 bits (76), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 5 RKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
+K+ Q AL + ++P +SE+E L L+ ++VR WF ++R
Sbjct: 14 KKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>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 = 33.5 bits (75), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 4 KRKTP------LQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
KRK P +Q L K + ++KY +E LA L +T QV+TWF +R
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 33.1 bits (74), Expect = 0.83, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
T +Q K L + Y+ K+ TK + ++A +L+ +QV WF +R ++K
Sbjct: 9 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 33.1 bits (74), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 4 KRKTPLQ--AK-ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
KR+T + AK AL + + E P+ E+ +A L+L + VR WF +R+R+K
Sbjct: 89 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 33.1 bits (74), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 10 QAKALLK--FYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
Q A+L+ F + K+P + +EGL+ LD + ++ WF ++R ++K
Sbjct: 10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
T +Q K L + Y+ K+ TK + ++A +L+ +QV WF +R ++K
Sbjct: 15 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>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 = 32.7 bits (73), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 29/50 (58%)
Query: 4 KRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53
K + P Q +AL +++ P E++ L + +T +++ +WF E+R++
Sbjct: 12 KERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 24/51 (47%)
Query: 5 RKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
R T Q + L F+ YP E E L+ L+L + + WF R++ +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>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 = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58
K++T ++ AL K + E + PT E+ +A L++ + +R WF +R+++K N
Sbjct: 106 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 163
>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 = 32.3 bits (72), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58
K++T ++ AL K + E + PT E+ +A L++ + +R WF +R+++K N
Sbjct: 98 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 155
>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 = 32.3 bits (72), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58
K++T ++ AL K + E + PT E+ +A L++ + +R WF +R+++K N
Sbjct: 105 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 162
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
K++T ++ AL K + E + PT E+ +A L++ + +R WF +R+++K
Sbjct: 9 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 23 YPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53
YP++ + + LA LT QV WFI RRR
Sbjct: 25 YPSEEQKKQLAQDTGLTILQVNNWFINARRR 55
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%)
Query: 9 LQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
Q AL + + + +Y E LAA+L LT QV+ WF KR + K
Sbjct: 17 FQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 24 PTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
P+ E+ GLA +L L + VR WF +R+++K
Sbjct: 124 PSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>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 = 31.6 bits (70), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58
K++T ++ AL K + E + PT E+ +A L++ + +R WF +R+++K N
Sbjct: 102 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRIN 159
>pdb|1JR9|A Chain A, Crystal Structure Of Manganese Superoxide Dismutases From
Bacillus Halodenitrificans
Length = 202
Score = 31.2 bits (69), Expect = 3.4, Method: Composition-based stats.
Identities = 16/34 (47%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 193 VRKHGMGKGLMTA-WRVMNPNGGTVPTGIDVADR 225
VR +G G + W++M+PNGG PTG +VAD+
Sbjct: 72 VRNNGGGHANHSLFWKLMSPNGGGKPTG-EVADK 104
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 31.2 bits (69), Expect = 3.9, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 4 KRKTPLQAKALLK--FYSE--EKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59
+R QA +L FYS YP++ E LA +T QV WF KR R K + G
Sbjct: 5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG 64
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
T Q L + + + +Y T + L+A L L QV+ WF +RRR K
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 30.8 bits (68), Expect = 4.4, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 4 KRKTPLQAKALLK--FYSE--EKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59
+R QA +L FYS YP++ E LA +T QV WF KR R K + G
Sbjct: 5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG 64
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 30.8 bits (68), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 23 YPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53
YP++ E + L+ +L+ Q+ WFI RRR
Sbjct: 34 YPSEEEKQMLSEKTNLSLLQISNWFINARRR 64
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.8 bits (68), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 18 YSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
+ +KY +E LA AL +T QV+TWF +R
Sbjct: 16 FLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.8 bits (68), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 10 QAKALL-KFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
QA+A L + + ++ E E +A +T QVR WFI KR R K
Sbjct: 7 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 24/42 (57%)
Query: 10 QAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
Q L K + +KY + E + LA L L+ +QV+TWF +R
Sbjct: 18 QTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRR 59
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.4 bits (67), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 KRKTPLQAK---ALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58
K++T ++ AL K + E + PT ++ +A L++ + +R WF +R+++K N
Sbjct: 103 KKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 160
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 30.4 bits (67), Expect = 6.1, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 4 KRKTPLQAKALLK--FYSE--EKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59
+R QA +L FYS YP++ E LA +T QV WF KR R K + G
Sbjct: 6 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKNIG 65
>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 = 30.4 bits (67), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 10 QAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
Q L + + +++Y + E + LA+ L LT QV+ WF +R + K
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 30.4 bits (67), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 10 QAKALL-KFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
QA+A L + + ++ E E +A +T QVR WFI KR R K
Sbjct: 15 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 30.0 bits (66), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 22/45 (48%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
T Q +AL + E KYP E LA + L ++V WF +R
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 30.0 bits (66), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKR 51
T Q +AL K + YP E LAA +DL +++ WF +R
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 30.0 bits (66), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 10 QAKALLK-FYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
QA+A L+ + ++ E E +A +T QVR WFI KR R K
Sbjct: 15 QARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 29.6 bits (65), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 18 YSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
+S +KY + E LA L LT QV+ WF +R + K
Sbjct: 23 FSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTK 60
>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 = 29.6 bits (65), Expect = 9.3, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 7 TPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53
T Q + L + +YP S E +A +LT +VR WF +R +
Sbjct: 11 TSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 57
>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 = 29.6 bits (65), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 10 QAKALL-KFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55
QA+A L + + ++ E E +A +T QVR WFI KR R K
Sbjct: 375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
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 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,250,365
Number of Sequences: 62578
Number of extensions: 1276087
Number of successful extensions: 3043
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 3001
Number of HSP's gapped (non-prelim): 56
length of query: 1159
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1050
effective length of database: 8,152,335
effective search space: 8559951750
effective search space used: 8559951750
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)