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= psy10105
(197 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of
Human Homeobox Protein Tgif1, Northeast Structural
Genomics Consortium Target Hr4411b
Length = 89
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/50 (48%), Positives = 33/50 (66%)
Query: 74 RESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 123
+ES L+ WL EH+ N YP++ EK +L+ T ++ QV WF NARRRL
Sbjct: 14 KESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRL 63
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 35/50 (70%)
Query: 74 RESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 123
+ +T +++WL +H +PYPT+ EK +A T +TL QV+ WF NARRR+
Sbjct: 16 KHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 54.3 bits (129), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 61 AGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120
+G R+ N ES L+ W+ +H+ YP++ EK ML+ T ++L Q+S WF NAR
Sbjct: 3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINAR 62
Query: 121 RRL 123
RR+
Sbjct: 63 RRI 65
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 33/48 (68%)
Query: 76 STATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 123
+T +AWL +H +PYP++ +K LA T +T+ QV+ WF NARRR+
Sbjct: 9 ATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+R+N +++T L + H NPYP++ K LA + +T++QVS WF N R R KK
Sbjct: 5 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 34/58 (58%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+R+N +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 34/58 (58%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+R+N +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 45.8 bits (107), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+R+N +++++ L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 32/56 (57%)
Query: 70 KNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
++ +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 76 STATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 122
S L+ W + NPYP+ EK LA T +T TQVS WF N R+R
Sbjct: 505 SRGVLREW---YAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 133
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 67
>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 = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 133
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 18 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 61
>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 = 34.7 bits (78), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R + KKENK
Sbjct: 6 RQTYTRYQTLELE---KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 129 MTWEP 133
EP
Sbjct: 63 TKGEP 67
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R +LKKE
Sbjct: 24 RQTYTRYQTLELE---KEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 32.0 bits (71), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 73 TRESTATLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 124
T+E+ L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 35 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 86
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R+ TR T L+ E N Y T+ +I +A +T Q+ WF N R + KKEN
Sbjct: 7 RQTYTRYQTLELEK---EFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>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 = 0.26, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 30/66 (45%)
Query: 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121
G ++ RK T S+ L A +K Y E+ LA +T TQV WF N R
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 122 RLKKEN 127
++KK
Sbjct: 61 KIKKSG 66
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
RRK S A + K+ Y + E+ LA + +T TQV WF N R ++K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 128 K 128
K
Sbjct: 62 K 62
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 80 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
L+A + +NP P E L TKMT ++ +WF+ R+++ E
Sbjct: 19 LRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 73 TRESTATLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 124
T+E+ L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 6 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 57
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 4/54 (7%)
Query: 73 TRESTATLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLK 124
T+E+ L++W ++ +NPY TKG E +M T ++ Q+ W +N RR+ K
Sbjct: 10 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVSNRRRKEK 61
>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 = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 25/54 (46%)
Query: 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120
RRK S A + K+ Y + E+ LA + K+T TQV WF N R
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 60 GAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANA 119
A + +R + TR T L+ E N Y T+ +I +A +T Q+ WF N
Sbjct: 23 NANGETKRQRTSYTRYQTLELEK---EFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79
Query: 120 RRRLKKENK 128
R + KKE+K
Sbjct: 80 RMKWKKEHK 88
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 30.8 bits (68), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
N Y T+ + +A + +T QV WF N R ++KK NK
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>pdb|3FWL|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 751
Score = 30.0 bits (66), Expect = 0.77, Method: Composition-based stats.
Identities = 28/115 (24%), Positives = 49/115 (42%), Gaps = 31/115 (26%)
Query: 32 VPALQSRRQLCGIDKQVIQVSNLTA-VRYG--------AGYDLA--ARRKNATRESTATL 80
+PAL+ +R+L ++ ++ V + VR AGY+ A ARR + AT
Sbjct: 405 IPALKKQRKLSDLETAIVVVDRFSGEVRAXVGGSEPQFAGYNRAXQARRSIGSLAKPATY 464
Query: 81 KAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 135
L++ K + +++TW A+A L++ N W P+N
Sbjct: 465 LTALSQPK--------------------IYRLNTWIADAPIALRQPNGQVWSPQN 499
>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 = 30.0 bits (66), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 16/32 (50%)
Query: 89 KNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120
K Y E+ LA KMT QV TWF N R
Sbjct: 38 KQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 30.0 bits (66), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
N Y T+ + +A + +T QV WF N R ++KK N
Sbjct: 23 NMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>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 = 30.0 bits (66), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 74 RESTATLKAWLNEHKK----NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
R TA +A L E +K N Y ++ ++ LA++ +T + WF N R + KKE
Sbjct: 5 RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 768
Score = 29.6 bits (65), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 28/116 (24%), Positives = 50/116 (43%), Gaps = 31/116 (26%)
Query: 32 VPALQSRRQLCGIDKQVIQVSNLT----AVRYG-----AGYDLA--ARRKNATRESTATL 80
+PAL+ +R+L ++ ++ V + A+ G AGY+ A ARR + AT
Sbjct: 422 IPALKKQRKLSDLETAIVVVDRFSGEVRAMVGGSEPQFAGYNRAMQARRSIGSLAKPATY 481
Query: 81 KAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNK 136
L++ K + +++TW A+A L++ N W P+N
Sbjct: 482 LTALSQPK--------------------IYRLNTWIADAPIALRQPNGQVWSPQND 517
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 89 KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
K+ +PT+ E L + TK++ ++ +WF+ RR+L+
Sbjct: 34 KSSFPTQAELDRLRVETKLSRREIDSWFSE-RRKLR 68
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129
++N YP + +A+ T +T +V WF N R + +K +
Sbjct: 23 QRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF 64
>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 = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129
++N YP + +A+ T +T +V WF N R + +K +
Sbjct: 23 QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF 64
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 89 KNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
+ Y E+ LA +MT QV TWF N R + +++
Sbjct: 18 RQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WF NAR ++KK
Sbjct: 11 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 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 = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WFAN R ++KK
Sbjct: 9 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R++ T S + L ++ YP + LA T +T ++ WF N R RL+K++
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>pdb|2BF1|A Chain A, Structure Of An Unliganded And Fully-Glycosylated Siv
Gp120 Envelope Glycoprotein
pdb|3FUS|A Chain A, Improved Structure Of The Unliganded Simian
Immunodeficiency Virus Gp120 Core
Length = 316
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 84 LNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 135
N+ + + K K++++ T+M TQ STWF R + + W ++
Sbjct: 83 CNDTNYSGFMPKCSKVVVSSCTRMMETQTSTWFGFNGTRAENRTYIYWHGRD 134
>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 = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 76 STATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
S A L A + +K Y + + L+ I ++ QV TWF N R + K+
Sbjct: 11 SQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 80 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 13 LKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 76 STATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
S L+ E+ N + TK ++ ++ T ++ Q++ WF N R + KK
Sbjct: 15 SKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 80 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
LK E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 19 LKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R+N T ++ L+ +K YP + LA+ T +T +V WF N R + +K
Sbjct: 9 KRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRE 68
Query: 128 KM 129
+
Sbjct: 69 RF 70
>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 = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
L+ RRK T T A +N PT E M+A M + WF N R++ K
Sbjct: 101 LSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
Query: 125 KEN 127
+ N
Sbjct: 161 RIN 163
>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 = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKN 135
N Y T+ +I +A ++ Q+ WF N R + KK+ + P++
Sbjct: 25 NRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRTLDSSPEH 70
>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 = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 92 YPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK-ENKMTWE 132
Y + E+ LA + ++T TQV WF N R + K+ +N+ +E
Sbjct: 33 YLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYE 74
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
N Y ++ ++ +A ++ TQV WF N R + KK +
Sbjct: 56 NKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 122
K+N P+K +I ++ + L+ VS +F NARRR
Sbjct: 117 KENKRPSKELQITISQQLGLELSTVSNFFMNARRR 151
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 24/53 (45%)
Query: 73 TRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
TR + L+ + N YP E L+ + + + WF NAR++ +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
L+ RRK T T A +N PT E M+A M + WF N R++ K
Sbjct: 100 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
Query: 125 KEN 127
+ N
Sbjct: 160 RIN 162
>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 = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
L+ RRK T T A +N PT E M+A M + WF N R++ K
Sbjct: 93 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
Query: 125 KEN 127
+ N
Sbjct: 153 RIN 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 = 27.3 bits (59), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 28/63 (44%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
L+ RRK T T A +N PT E M+A M + WF+N R++ K
Sbjct: 97 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
Query: 125 KEN 127
+ N
Sbjct: 157 RIN 159
>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 = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + QV WF N R ++KK
Sbjct: 14 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>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 = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 11 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121
G ++ ++N T + ++A E ++ YP + LA + ++ WF+N R
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 122 RLKKENKM 129
+ ++E K+
Sbjct: 61 KWRREEKL 68
>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 = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 13 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 73 TRESTATLKAWLNEHKKNPY-PTKG-EKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 130
T+E+ L++W ++ +NPY TKG E +M T ++ Q+ W A ARR KE +T
Sbjct: 10 TKENVRILESWFAKNIENPYLDTKGLENLMKN--TSLSRIQIKNWVA-ARR--AKEKTIT 64
Query: 131 WEPK 134
P+
Sbjct: 65 IAPE 68
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 11 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 26.6 bits (57), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 75 ESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
E A LK NE N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 13 EQLARLKREFNE---NRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 26.6 bits (57), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
RK T +TA L A + ++ Y + E+ + +T TQV WF N R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 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
0.316 0.128 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,819,063
Number of Sequences: 62578
Number of extensions: 137552
Number of successful extensions: 354
Number of sequences better than 100.0: 71
Number of HSP's better than 100.0 without gapping: 65
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 286
Number of HSP's gapped (non-prelim): 71
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
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: 49 (23.5 bits)