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= psy4272
(575 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 72.0 bits (175), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 32/55 (58%), Positives = 41/55 (74%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
Y+ HQ +ELEKEF YL DRR +++ L LTERQ+KIWFQNRRMK+K+ + D
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 41/56 (73%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R RQ Y+ +Q +ELEKEF +YL RR ++ L LTERQIKIWFQNRRMKLK+
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 30/53 (56%), Positives = 40/53 (75%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382
Y+ +Q +ELEKEF YL DRR +++ L LTERQ+KIWFQNRRMK+K+ +
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>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 = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/60 (56%), Positives = 40/60 (66%)
Query: 323 TGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382
T R R Y+ +Q +ELEKEF YL RR ++ L LTERQIKIWFQNRRMK K+ H
Sbjct: 28 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87
>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 = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/56 (58%), Positives = 39/56 (69%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R RQ Y+ +Q +ELEKEF YL RR ++ L LTERQIKIWFQNRRMK K+
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/56 (58%), Positives = 39/56 (69%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R RQ Y+ +Q +ELEKEF YL RR ++ L LTERQIKIWFQNRRMK K+
Sbjct: 5 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>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 = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/56 (58%), Positives = 39/56 (69%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R RQ Y+ +Q +ELEKEF YL RR ++ L LTERQIKIWFQNRRMK K+
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>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 = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 41/59 (69%)
Query: 322 NTGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
++ R RQ Y+ +Q +ELEKEF Y+ RR ++ L L+ERQIKIWFQNRRMK K+
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
R +YSS Q+ L++ F+ T YL R L+ LGLT+ Q+KIWFQN+R K+K++ P
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPS 68
>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 = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/52 (57%), Positives = 36/52 (69%)
Query: 329 VYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
Y+ +Q +ELEKEF YL RR ++ L LTERQIKIWFQNRRMK K+
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 38/55 (69%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWFQN+R K+K++
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59
>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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 38/55 (69%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWFQN+R K+K++
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>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 = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/56 (55%), Positives = 37/56 (66%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R R Y+ Q++ELEKEF Y+ RR L+ L LTER IKIWFQNRRMK K+
Sbjct: 5 RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 37/55 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWFQN R K+K++
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 37/55 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWFQN R K+K++
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 37/55 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ ++EF YL RR+ LS ELGL E QIKIWFQN+R K++R+
Sbjct: 7 RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 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 = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 38/55 (69%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWF+N+R K+K++
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 44/64 (68%), Gaps = 1/64 (1%)
Query: 322 NTGRFRQV-YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
++GR +++ YS Q+ ELE+E+ ++ D+R+ +S L+ERQI IWFQNRR+K K+
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 381 THPD 384
+ P
Sbjct: 65 SGPS 68
>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 = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 37/55 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWF N+R K+K++
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 58.9 bits (141), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 28/54 (51%), Positives = 37/54 (68%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
+S+ Q +ELEK+F YL RK L+K L L+ERQ+K WFQNRR K +R+ P
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP 67
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/52 (53%), Positives = 35/52 (67%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKL 378
R +SS Q+ L++EF YL RR+ LS ELGL E QIKIWFQN+R K+
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 49/87 (56%), Gaps = 6/87 (6%)
Query: 294 LDLSQIPKPPPSSSHTYSNQIHKNLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPSDRR 353
D ++ + PP ++ ++ + L +G R +++ Q+ ELEKEF YL RR
Sbjct: 11 FDWMKVKRNPPKTA-----KVSEPGLGSPSG-LRTNFTTRQLTELEKEFHFNKYLSRARR 64
Query: 354 KVLSKELGLTERQIKIWFQNRRMKLKR 380
++ L L E Q+KIWFQNRRMK K+
Sbjct: 65 VEIAATLELNETQVKIWFQNRRMKQKK 91
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/62 (46%), Positives = 37/62 (59%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
R R ++S Q++ELEKEF YL R ++ L L+E Q+KIWFQNRR K KR
Sbjct: 9 RRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAG 68
Query: 385 MV 386
V
Sbjct: 69 NV 70
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 55.5 bits (132), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 39/59 (66%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
R R V++ Q++ LEK F YL + R L++ LGL++ Q+K W+QNRRMK K++ P
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77
>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 = 55.5 bits (132), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +SS Q+ L++EF YL RR+ LS ELGL E Q+K WF+N R K+K++
Sbjct: 8 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKS 62
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/47 (55%), Positives = 33/47 (70%)
Query: 334 QIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
Q++ELE++F YL + R L+K L LTE Q+KIWFQNRR K KR
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 36/56 (64%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R+R ++ Q+ LEKEF NY+ RR L+ +L L E IK+WFQNRRMK KR
Sbjct: 3 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
+++ Q++ LE++FR YL R S L LTE Q+KIWFQNRR K KR
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
+S Q++ELE+ F YL S R L+K L +T+ Q+K WFQNRR K +R
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 324 GRFRQV-YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
GR ++V Y+ Q+ ELE+E+ ++ D+R+ +S L+ERQ+ IWFQNRR+K K+
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 324 GRFRQV-YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
GR ++V Y+ Q+ ELE+E+ ++ D+R+ +S L+ERQ+ IWFQNRR+K K+
Sbjct: 1 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>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 = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R ++ Q+ ELEK F YL S R L++ L +T+ Q+K WFQNRR K +R
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 39/56 (69%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R+R ++S Q+ ELEK F T+Y R+ L+ ++GLTE +I++WFQNRR K ++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>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 = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 39/56 (69%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R+R ++S Q+ ELEK F T+Y R+ L+ ++GLTE +I++WFQNRR K ++
Sbjct: 8 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/42 (57%), Positives = 30/42 (71%)
Query: 340 KEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
+EF YL RR+ LS ELGL E QIKIWFQN+R K+K++
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 36/58 (62%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
R ++S Q+ ELE+ F+ YL + R+ L+ + LT Q+KIWFQN R K+KR D
Sbjct: 6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63
>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 = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
R R +S+ Q+ ELE+ F T Y R+ L++ LTE +I++WFQNRR +L++ H
Sbjct: 20 RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79
Query: 385 M 385
+
Sbjct: 80 V 80
>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 = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 33/53 (62%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
R ++S Q+ ELE+ F+ YL + R L+ L LT Q+KIWFQNRR K K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 36/51 (70%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
++S Q+ ELEK F T+Y R+ L+ ++GLTE +I++WFQNRR K ++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/55 (45%), Positives = 33/55 (60%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
R R ++S QI ELE+ F YL + R LS +L L Q+KIWF+NRR + K
Sbjct: 4 RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382
R ++ +QI LE FR+ Y D + L+++L L +I+IWFQNRR KLKR+H
Sbjct: 5 RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R +++ Q ELE+ FR YL + R+ L+ + LT Q+KIWFQN R K KR
Sbjct: 16 RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>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 = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRT 381
R +++ Q ELE+ FR YL + R+ L+ + LT Q+KIWFQN R K KR
Sbjct: 13 RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 34/58 (58%)
Query: 327 RQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPD 384
R V+SS Q+ L F+ YL + + LS L L+ +Q+K WFQN+RMK KR +
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 37/56 (66%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R R ++S+Q+ ELEK F+ T+Y R+ L+ LTE ++++WFQNRR K ++
Sbjct: 11 RNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
>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 = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
+ R V+S Q+ L+ F+ YL + + LS L L+ +Q+K WFQN+RMK KR
Sbjct: 5 KMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 37/59 (62%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
R R +++ Q+ LE F+ T Y R+ L++++ L E ++++WF+NRR K +R+ P
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R R ++ QI LEKEF T+Y R+ L+ ++ L E +I++WF NRR K +R
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 33/56 (58%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R R + HQ+ ++ F + + + K L+++ GLT+R +++WFQN R K +R
Sbjct: 9 RMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
R R +++ Q+ ELE+ F T+Y R+ L++ LTE ++++WF NRR + ++
Sbjct: 4 RSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 35/59 (59%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVVE 388
++S Q+ ELE F+ +Y R+ ++ LTE ++++WF+NRR K ++ +V +
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIVTD 68
>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 = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHPDMVVE 388
++S Q+ ELE F+ Y R+ ++ LTE ++++WF+NRR K ++ +V +
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIVTD 68
>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 = 36.6 bits (83), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 338 LEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
LE+ FR L S ++ ++K+ G+T Q+++WF N+RM+ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 35.8 bits (81), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 338 LEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
LE+ FR L S ++ ++K+ G+T Q+++WF N+RM+ K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 35.4 bits (80), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 338 LEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
LE+ FR L S ++ ++K+ G+T Q+++WF N+RM+ K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.4 bits (80), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 338 LEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
LE+ FR L S ++ ++K+ G+T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 330 YSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
++ +Q+ L+ F Y D + LS L L R I +WFQN R K +++ P
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 67
>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 = 33.9 bits (76), Expect = 0.25, Method: Composition-based stats.
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 365 RQIKIWFQNRRMKLKR 380
RQIKIWFQNRRMK K+
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 118 LTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHVTFKHAA 172
C CG+S+ R L H+ P +PC YC R K D+KKH TF H
Sbjct: 2 FDCKICGKSFKRSSTLSTHLLIHSDTRP-YPCQYCGKRFHQKSDMKKH-TFIHTG 54
>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 = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 336 VELEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
V LEK F L N P S+ +++ +L + + I++WF NRR K KR +P
Sbjct: 117 VALEKSF-LENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 164
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 33.5 bits (75), Expect = 0.33, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 325 RFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLK 379
R R ++ Q+ LE F T Y R+ ++ ++ L E ++++WF+NRR K +
Sbjct: 9 RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 365 RQIKIWFQNRRMKLKR 380
RQIKIWFQNRRMK K+
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>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 = 33.1 bits (74), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 336 VELEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
V LEK F L N P S+ +++ +L + + I++WF NRR K KR +P
Sbjct: 116 VALEKSF-LENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 163
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 338 LEKEF-RLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
LEK F +T Y R K LSK+L + R+I+ WF++RR + K + P
Sbjct: 23 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69
>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 = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 336 VELEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
V LEK F L N P S+ +++ +L + + I++WF NRR K KR +P
Sbjct: 109 VALEKSF-LENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 156
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 334 QIVELEKEF---RLTNYLPSDRRKV-LSKELGLTERQIKIWFQNRRMKLKR 380
Q E+ E+ L+N PS+ K L+K+ G+T Q+ WF N+R++ K+
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345 In
Zinc Finger Protein 278
Length = 95
Score = 32.0 bits (71), Expect = 0.84, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 115 AQGLTCLQCGRSYCRPYNLKRHIQYECGKAPQFPCLYCSYRARHKHDLKKHV 166
+ G+ C CG+ + Y+L RH G+ P + C C R + K + HV
Sbjct: 5 SSGVACEICGKIFRDVYHLNRHKLSHSGEKP-YSCPVCGLRFKRKDRMSYHV 55
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 32.0 bits (71), Expect = 0.89, Method: Composition-based stats.
Identities = 13/15 (86%), Positives = 14/15 (93%)
Query: 366 QIKIWFQNRRMKLKR 380
QIKIWFQNRRMK K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 344 LTNYLPSDRRKV-LSKELGLTERQIKIWFQNRRMKLKR 380
L+N PS+ K L+K+ G+T Q+ WF N+R++ K+
Sbjct: 24 LSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 2/47 (4%)
Query: 338 LEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
LEK F L N P S+ +++++L + + I++WF NRR K KR +P
Sbjct: 16 LEKSF-LANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRINP 61
>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 = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 336 VELEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382
V LEK F L N P S+ +++ +L + + I++WF NRR K KR +
Sbjct: 113 VALEKSF-LENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRIN 159
>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 = 1.9, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 10/63 (15%)
Query: 323 TGRFRQVYSSHQIVELEKEFRLTNYLPSDRRKVLSKE-----LGLTERQIKIWFQNRRMK 377
T R R V + Q+ L T Y + R L KE GL+ R I++WFQN+R K
Sbjct: 3 TTRVRTVLNEKQLHTLR-----TCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57
Query: 378 LKR 380
K+
Sbjct: 58 DKK 60
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 21/28 (75%)
Query: 356 LSKELGLTERQIKIWFQNRRMKLKRTHP 383
++ E+GL +R +++WFQN R + +++ P
Sbjct: 50 IAHEVGLKKRVVQVWFQNTRARERKSGP 77
>pdb|4GQW|A Chain A, Crystal Structure Of Cbs-pair Protein, Cbsx1 (loop
Deletion) From Arabidopsis Thaliana
Length = 152
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 60 ADVATKTLPVIQELLSQRDGKPVGKATLPSPL 91
D KT +Q+LLS+ +GK VG P+PL
Sbjct: 65 GDSTWKTFNAVQKLLSKTNGKLVGDLMTPAPL 96
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 344 LTNYLPSDRRKV-LSKELGLTERQIKIWFQNRRMKLKRT 381
L+N PS+ K L+K+ G+T Q+ WF N+R++ K+
Sbjct: 24 LSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
>pdb|3QJG|A Chain A, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|B Chain B, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|C Chain C, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|D Chain D, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|E Chain E, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|F Chain F, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|G Chain G, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|H Chain H, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|I Chain I, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|J Chain J, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|K Chain K, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
pdb|3QJG|L Chain L, Epidermin Biosynthesis Protein Epid From Staphylococcus
Aureus
Length = 175
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 311 SNQIHKNLLQCNTGRFRQVYSSHQIVELEKEFRLTNYLPS-DRRKVLSKEL 360
SN + +N+L C G + SH I+EL+ +F N + S + RK ++ E+
Sbjct: 1 SNAMGENVLICLCGSVNSINISHYIIELKSKFDEVNVIASTNGRKFINGEI 51
>pdb|4GQV|A Chain A, Crystal Structure Of Cbs-pair Protein, Cbsx1 From
Arabidopsis Thaliana
Length = 166
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 61 DVATKTLPVIQELLSQRDGKPVGKATLPSPL 91
D KT +Q+LLS+ +GK VG P+PL
Sbjct: 80 DSTWKTFNAVQKLLSKTNGKLVGDLMTPAPL 110
>pdb|4F0J|A Chain A, Crystal Structure Of A Probable Hydrolytic Enzyme (Pa3053)
From Pseudomonas Aeruginosa Pao1 At 1.50 A Resolution
Length = 315
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 73 LLSQRDGKPVGKATLPSPLKAKLSDYENKMKNVRESIRQKRLAQ 116
L+ ++D +GK P+ LKA+L +Y K+ I Q L +
Sbjct: 244 LIGEKDNTAIGKDAAPAELKARLGNYAQLGKDAARRIPQATLVE 287
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 336 VELEKEFRLTNYLPSDRRKVLSKELGLTERQIKIWFQNRRMKLKRTH 382
V LEK F S+ +++++L + + I++WF NRR K KR +
Sbjct: 114 VALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 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 = 3.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 344 LTNYLPSDRRKV-LSKELGLTERQIKIWFQNRRMKLKR 380
L+N PS+ K L+K+ G+T Q+ WF N+R++ K+
Sbjct: 25 LSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 356 LSKELGLTERQIKIWFQNRRMKLKRT 381
++ +LGL + +++WF NRR K KR+
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKRS 154
>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 = 29.3 bits (64), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 344 LTNYLPSDRRKV-LSKELGLTERQIKIWFQNRRMKLKRT 381
L+N PS+ K L+++ G+T Q+ WF N+R++ K+
Sbjct: 24 LSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKN 62
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 340 KEFRLTNYLPSDRRK-VLSKELGLTERQIKIWFQNRRMK 377
+E+ N PS R K L++ GLT Q+ WF+NRR +
Sbjct: 510 REWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 336 VELEKEFRLTNYLP-SDRRKVLSKELGLTERQIKIWFQNRRMKLKR 380
V LEK F L N P S+ +++ +L + + I++WF NRR K KR
Sbjct: 20 VALEKSF-LENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 29.3 bits (64), Expect = 7.0, Method: Composition-based stats.
Identities = 13/16 (81%), Positives = 15/16 (93%)
Query: 365 RQIKIWFQNRRMKLKR 380
RQIKI+FQNRRMK K+
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 356 LSKELGLTERQIKIWFQNRRMKLKRT 381
++ +LGL + +++WF NRR K KR+
Sbjct: 41 IANQLGLEKDVVRVWFCNRRQKGKRS 66
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 28.5 bits (62), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 338 LEKEFRLTNYLPSDRR-KVLSKELGLTERQIKIWFQNRRMKLKRTHP 383
LEK F P ++R + LSK+L R I+ WF+ RR + K + P
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGP 61
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
0.312 0.128 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,538,796
Number of Sequences: 62578
Number of extensions: 600433
Number of successful extensions: 1284
Number of sequences better than 100.0: 115
Number of HSP's better than 100.0 without gapping: 89
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 1180
Number of HSP's gapped (non-prelim): 126
length of query: 575
length of database: 14,973,337
effective HSP length: 104
effective length of query: 471
effective length of database: 8,465,225
effective search space: 3987120975
effective search space used: 3987120975
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)