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= psy3400
(417 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 295 bits (755), Expect = 3e-80, Method: Compositional matrix adjust.
Identities = 141/160 (88%), Positives = 148/160 (92%)
Query: 203 SEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFK 262
S+EDAP+SDDLE FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFK
Sbjct: 5 SDEDAPSSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFK 64
Query: 263 NMCKLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKP 322
NMCKLKPLL KWLEE DS++GSPT++DKIAAQGRKRKKRTSIEV VKGALE+HF K PKP
Sbjct: 65 NMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKP 124
Query: 323 SAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362
SA EIT LADSLQLEKEVVRVWFCNRRQKEKRMTP G
Sbjct: 125 SAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAAGAG 164
>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 = 204 bits (518), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 98/163 (60%), Positives = 119/163 (73%), Gaps = 7/163 (4%)
Query: 202 GSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSF 261
GS E+ ++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSF
Sbjct: 1 GSREEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSF 60
Query: 262 KNMCKLKPLLQKWLEEADSTTGSPTSIDK-------IAAQGRKRKKRTSIEVTVKGALET 314
KNMCKLKPLL+KWL +A++ + + I R+RKKRTSIE ++ ALE
Sbjct: 61 KNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEK 120
Query: 315 HFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
F + KP+++EIT +AD L +EKEV+RVWFCNRRQKEKR+ P
Sbjct: 121 SFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 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 = 200 bits (508), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 95/154 (61%), Positives = 115/154 (74%), Gaps = 7/154 (4%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNMCKLKPL
Sbjct: 3 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPL 62
Query: 271 LQKWLEEADSTTGSPTSIDK-------IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPS 323
L+KWL +A++ + + I R+RKKRTSIE ++ ALE F + KP+
Sbjct: 63 LEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPT 122
Query: 324 AQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
++EIT +AD L +EKEV+RVWFCNRRQKEKR+ P
Sbjct: 123 SEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 156
>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 = 198 bits (503), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 99/172 (57%), Positives = 120/172 (69%), Gaps = 14/172 (8%)
Query: 196 HPDAPSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
H + PS EE LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFE
Sbjct: 3 HMEEPSDLEE-------LEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFE 55
Query: 256 ALQLSFKNMCKLKPLLQKWLEEADSTTGSPTSIDK-------IAAQGRKRKKRTSIEVTV 308
AL LSFKNM KLKPLL+KWL +A++ + + I +RKKRTSIE +
Sbjct: 56 ALNLSFKNMAKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSERRKKRTSIETNI 115
Query: 309 KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360
+ ALE F + KP+++EIT +AD L +EKEV+RVWFCNRRQKEKR+ PP++
Sbjct: 116 RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINPPSS 167
>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 = 190 bits (483), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 92/152 (60%), Positives = 112/152 (73%), Gaps = 7/152 (4%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNM KLKPL
Sbjct: 7 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPL 66
Query: 271 LQKWLEEADSTTGSPTSIDK-------IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPS 323
L+KWL +A++ + + I R+RKKRTSIE ++ ALE F + KP+
Sbjct: 67 LEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPT 126
Query: 324 AQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
++EIT +AD L +EKEV+RVWF NRRQKEKR+
Sbjct: 127 SEEITMIADQLNMEKEVIRVWFSNRRQKEKRI 158
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 187 bits (476), Expect = 8e-48, Method: Compositional matrix adjust.
Identities = 92/153 (60%), Positives = 114/153 (74%), Gaps = 8/153 (5%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNM KLKPL
Sbjct: 7 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPL 66
Query: 271 LQKWLEEADSTTGSPTSIDK--------IAAQGRKRKKRTSIEVTVKGALETHFHKQPKP 322
L+KWL +A++ S +S+ I R+RKKRTSIE ++ ALE F + KP
Sbjct: 67 LEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKP 126
Query: 323 SAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
++++IT +A+ L +EKEV+RVWF NRRQKEKR+
Sbjct: 127 TSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 186 bits (472), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 89/143 (62%), Positives = 110/143 (76%), Gaps = 2/143 (1%)
Query: 213 LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQ 272
LE FA +FK RRIKLG+TQ +VG AL ++G+ FSQTTICRFE LQLSFKN CKLK +L
Sbjct: 5 LEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILS 64
Query: 273 KWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLAD 332
KWLEEA+ G+ + +K+ A RKRK+RT+I + K ALE HF + KPS+QEI +A+
Sbjct: 65 KWLEEAEQ-VGALYN-EKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAE 122
Query: 333 SLQLEKEVVRVWFCNRRQKEKRM 355
L LEKEVVRVWFCNRRQ+EKR+
Sbjct: 123 ELNLEKEVVRVWFCNRRQREKRV 145
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 182 bits (461), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 94/154 (61%), Positives = 111/154 (72%), Gaps = 2/154 (1%)
Query: 202 GSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSF 261
G+ + +LE FAK KQ+RI LG+TQADVGL LG L+G VFSQTTI RFEALQLS
Sbjct: 1 GAMDMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSL 60
Query: 262 KNMCKLKPLLQKWLEEADSTTG-SPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQP 320
KNM KL+PLL+KW+EEAD+ S + Q RKR KRTSIE V+ +LET F K P
Sbjct: 61 KNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKR-KRTSIENRVRWSLETMFLKSP 119
Query: 321 KPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
KPS Q+IT +A+ L LEK+VVRVWF NRRQK KR
Sbjct: 120 KPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|1POU|A Chain A, The Solution Structure Of The Oct-1 Pou-Specific Domain
Reveals A Striking Similarity To The Bacteriophage
Lambda Repressor Dna-Binding Domain
Length = 71
Score = 121 bits (304), Expect = 6e-28, Method: Composition-based stats.
Identities = 55/69 (79%), Positives = 61/69 (88%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
++LE FAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNMCKLKPL
Sbjct: 3 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPL 62
Query: 271 LQKWLEEAD 279
L+KWL +A+
Sbjct: 63 LEKWLNDAE 71
>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 = 115 bits (288), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 63/143 (44%), Positives = 85/143 (59%), Gaps = 3/143 (2%)
Query: 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPL 270
+++ FAK FK RR+ LG TQ VG A G +SQ+ I RFE L ++ K+ KLKP+
Sbjct: 4 EEIREFAKNFKIRRLSLGLTQTQVGQAXTATEGPAYSQSAISRFEKLDITPKSAQKLKPV 63
Query: 271 LQKWLEEAD--STTGSPTSIDKIAAQ-GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEI 327
L+KWL EA+ + G + + + +KRK+RTS AL +F K P P+ QEI
Sbjct: 64 LEKWLNEAELRNQEGQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEI 123
Query: 328 TTLADSLQLEKEVVRVWFCNRRQ 350
T A L ++EVVRVWF NRRQ
Sbjct: 124 TEXAKELNYDREVVRVWFSNRRQ 146
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 90.1 bits (222), Expect = 2e-18, Method: Composition-based stats.
Identities = 38/60 (63%), Positives = 49/60 (81%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
R+RKKRTSIE ++ ALE F + KP+++EIT +AD L +EKEV+RVWFCNRRQKEKR+
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 65
>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 = 86.7 bits (213), Expect = 2e-17, Method: Composition-based stats.
Identities = 37/61 (60%), Positives = 47/61 (77%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
+RKKRTSIE V+ ALE F KP+++EI +A+ L +EKEV+RVWFCNRRQKEKR+
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRIN 60
Query: 357 P 357
P
Sbjct: 61 P 61
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 82.8 bits (203), Expect = 4e-16, Method: Composition-based stats.
Identities = 42/61 (68%), Positives = 48/61 (78%), Gaps = 1/61 (1%)
Query: 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
Q RKRK RTSIE V+ +LET F K PKPS Q+IT +A+ L LEK+VVRVWFCNRRQK K
Sbjct: 6 QARKRK-RTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
Query: 354 R 354
R
Sbjct: 65 R 65
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 37/68 (54%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
A G+ R++RT+ LE FH + S E + +A +L+L + V++WF NRR K
Sbjct: 2 APGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
Query: 352 EKRMTPPN 359
KR+ N
Sbjct: 62 WKRIKAGN 69
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 32/61 (52%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
+++K RTS LE FHKQ ++ E LA L++ V+ WF NRR K +R
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
Query: 356 T 356
T
Sbjct: 76 T 76
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
R+ RT+ G LE F+K+ S LA L L + ++VWF NRR K+KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 31/60 (51%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G K+K RT AL+ F KQ S Q++ L+ L L + V+ WF N+R K KR
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 29/58 (50%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
RK RT ALE F ++ S E + SL L + V++WF NRR K KR+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 285 PTSIDKIAAQG------RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEK 338
PTS + A+ +K+K RT T L F +Q S Q++ L++ L L
Sbjct: 4 PTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSY 63
Query: 339 EVVRVWFCNRRQKEKRMTPPN 359
+ V+ WF N+R K KR N
Sbjct: 64 KQVKTWFQNQRMKSKRWQKNN 84
>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 = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/51 (43%), Positives = 28/51 (54%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362
LE F Q SA E LA +L+L + V++WF NRR K KR + LG
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG 69
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
R+ RT+ LE F P + LA L LE + +++WF NRR K KR
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>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 = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 266 KLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQ 325
K P + W++ T + + A G +++RTS LE FH + +
Sbjct: 3 KNPPQIYPWMKRVHLGTST------VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRR 56
Query: 326 EITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+A +L L + +++WF NRR K K+
Sbjct: 57 RRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>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 = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 27/57 (47%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
+RK R LE F +Q SA E LA L+L V++WF NRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 31/64 (48%)
Query: 291 IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
++ +G+KR+ RT+ LE F K P LA L + V+VWF NRR
Sbjct: 3 MSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRA 62
Query: 351 KEKR 354
K ++
Sbjct: 63 KWRK 66
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 27/60 (45%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
R+ RT ALE F + P LA + L +E V VWF NRR K +R P
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
>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 = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 29/59 (49%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+KRK+R LE F +Q SA E LA ++L V++WF N R K KR
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 35.8 bits (81), Expect = 0.043, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
LE F +Q ++ E LA +L++ V+ WF NRR K +R T
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 35.8 bits (81), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
A +GR R + E+ + G LE F KQ S + LA+SL L + V+ W+ NRR K
Sbjct: 14 AKKGR-RSRTVFTELQLMG-LEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
Query: 352 EKRMTP 357
K+ P
Sbjct: 72 WKKSGP 77
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
++ RTS + ++++F P A+++ LA L K V++VWF N R K +R
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 358 PNTLGG 363
GG
Sbjct: 68 RQENGG 73
>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 = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 31/64 (48%)
Query: 291 IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350
IA + ++R+ RT+ + LE F + P LA L + ++VWF NRR
Sbjct: 12 IALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRA 71
Query: 351 KEKR 354
+ ++
Sbjct: 72 RLRK 75
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 29/60 (48%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
RK RT AL+ F K + E LA SL L + V++WF N+R K K+ P
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 35.0 bits (79), Expect = 0.081, Method: Composition-based stats.
Identities = 20/46 (43%), Positives = 23/46 (50%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
LE F Q S E LA LQL + V+ WF NRR K +R P
Sbjct: 22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP 67
>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 = 35.0 bits (79), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 24/34 (70%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWF 345
L+ ++ +PSA+E++ +ADS+ L +VV+ WF
Sbjct: 18 LKAYYALNAQPSAEELSKIADSVNLPLDVVKKWF 51
>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 = 34.7 bits (78), Expect = 0.094, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 23/43 (53%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
L T + P+P A L + L V+RVWF N+R K+K+
Sbjct: 18 LRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 27/58 (46%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+RK+R LE F +Q SA E LA + L V++WF N R K KR
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59
>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 = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 27/60 (45%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G +R++RT LE F + P +A L + VRVWF NRR K ++
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 27/60 (45%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G +R++RT LE F + P +A L + VRVWF NRR K ++
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
R+ RT+ + LE HF + +A + L+ L L V++WF NRR++ K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 42/103 (40%), Gaps = 24/103 (23%)
Query: 270 LLQKWLE----EADSTTGSPTSIDKIAAQGRKRKKRT---------------SIEVTVKG 310
L Q WL+ EA+ G P + A G+ R +R + +G
Sbjct: 453 LQQLWLKAHYVEAEKLRGRP-----LGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRG 507
Query: 311 ALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
L + P PS +E LA++ L V WF NRRQ+++
Sbjct: 508 VLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 29/63 (46%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
G +R+ R + LE FH + + +A +L L + +++WF NRR K
Sbjct: 15 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 352 EKR 354
K+
Sbjct: 75 LKK 77
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
RT+ LE FH S +A +L+L + V++WF NRR K+K+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 22/46 (47%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
L+ F P E L++ L L V+ VWF N RQK ++ P
Sbjct: 22 LQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 67
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK---EKR 354
++ RTS ALE F + P LA + L + ++VWF NRR K E++
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 355 MTPPNTLGGPQDG 367
+ GP G
Sbjct: 68 LRNQRRQSGPSSG 80
>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 = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
LE FH + + +A++L L + +++WF NRR K K+
Sbjct: 18 LEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+KRK+R LE F +Q SA E L ++L V++WF N R K KR
Sbjct: 10 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
+R+ RT+ LE F + P LA +L + V+VWF NRR + ++
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
RKR ++T LE FH + + +A +L L + +++WF NRR K K+
Sbjct: 3 RKRGRQTYTRYQTL-ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>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 = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
RKR ++T LE FH + + +A +L L + +++WF NRR K K+
Sbjct: 2 RKRGRQTYTRYQTL-ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>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 = 32.3 bits (72), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 311 ALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
ALE+ F + P P +E+ L ++ + + WF RR+K
Sbjct: 21 ALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
++ RT I L +F PS ++I +AD L ++V++ WF N KE++ P
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 67
>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 = 31.6 bits (70), Expect = 0.95, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
RKR ++T LE FH + + +A +L L + +++WF NRR K K+
Sbjct: 2 RKRGRQTYTRYQTL-ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>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 = 31.6 bits (70), Expect = 0.95, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 312 LETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
LE FH + + +A +L L + +++WF NRR K K+
Sbjct: 11 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>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 = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 30/63 (47%)
Query: 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351
A + ++R+ RT+ LE F + P LA + L + ++VWF NRR K
Sbjct: 1 APKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60
Query: 352 EKR 354
++
Sbjct: 61 WRK 63
>pdb|2DA4|A Chain A, Solution Structure Of The Homeobox Domain Of The
Hypothetical Protein, Dkfzp686k21156
Length = 80
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLGGPQDG 367
++I +A L ++ E+VR W NRR+K + M + GP G
Sbjct: 40 EKIEAVATELNVDCEIVRTWIGNRRRKYRLMGI--EVSGPSSG 80
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 299 KKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
K ++SI + LE F ++ +++E +A + VRVWF N+R + K
Sbjct: 7 KGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 299 KKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
K ++SI + LE F ++ +++E +A + VRVWF N+R + K
Sbjct: 7 KGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2P22|D Chain D, Structure Of The Yeast Escrt-i Heterotetramer Core
Length = 79
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 242 YGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEADSTT 282
YG F Q T+ RF+ + + + LL W EE D+ T
Sbjct: 16 YGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYEECDNIT 56
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
++SI + LE F ++ +++E +A + VRVWF N+R + K
Sbjct: 1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 330 LADSLQLEKEVVRVWFCNRRQKEKRM 355
+A L L + V++WF NRR K K+M
Sbjct: 34 VARVLNLTERQVKIWFQNRRMKMKKM 59
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 1/74 (1%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357
R++RT+ LE F K P +A + L + V+VWF NRR K ++
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 358 PNTLGGPQDGMMEG 371
GG Q G G
Sbjct: 68 QQQNGG-QSGPSSG 80
>pdb|2B6H|A Chain A, Structure Of Human Adp-Ribosylation Factor 5
Length = 192
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 32/153 (20%), Positives = 64/153 (41%), Gaps = 28/153 (18%)
Query: 216 FAKQFKQRRIKLGFTQADVGLALGTLY----GNVFSQTTICRFEALQLSFKNMC------ 265
F++ F ++++++ D LY G + + F + +KN+C
Sbjct: 21 FSRIFGKKQMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNICFTVWDV 80
Query: 266 ----KLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEV-------TVKGALET 314
K++PL W +T G +D + R+R + ++ E+ ++ A+
Sbjct: 81 GGQDKIRPL---WRHYFQNTQGLIFVVD---SNDRERVQESADELQKMLQEDELRDAVLL 134
Query: 315 HF-HKQPKPSAQEITTLADSLQLEKEVVRVWFC 346
F +KQ P+A ++ L D L L+ R W+
Sbjct: 135 VFANKQDMPNAMPVSELTDKLGLQHLRSRTWYV 167
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 28.9 bits (63), Expect = 5.1, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 30/60 (50%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356
+++ RT+ L+ F++ + + L+ L L + +++WF N+R K K+ T
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 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 = 28.9 bits (63), Expect = 5.1, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 26/60 (43%)
Query: 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
G ++ RT+ LE F S LA L L + +++WF NRR K K+
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
RKKR LE + + + ++ + L + V +WF NRR KEK++
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.9 bits (63), Expect = 5.8, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 26/58 (44%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
RKKR LE + + + ++ + L + V +WF NRR KEK++
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 28.5 bits (62), Expect = 7.2, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 281 TTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEV 340
++GS + A Q K K + +++ LE F K P+ E+ L +L +
Sbjct: 2 SSGSSGAYPDFAPQKFKEKTQGQVKI-----LEDSFLKSSFPTQAELDRLRVETKLSRRE 56
Query: 341 VRVWFCNRRQKEKRM 355
+ WF RR+ M
Sbjct: 57 IDSWFSERRKLRDSM 71
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 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,743,193
Number of Sequences: 62578
Number of extensions: 449565
Number of successful extensions: 749
Number of sequences better than 100.0: 74
Number of HSP's better than 100.0 without gapping: 66
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 673
Number of HSP's gapped (non-prelim): 76
length of query: 417
length of database: 14,973,337
effective HSP length: 101
effective length of query: 316
effective length of database: 8,652,959
effective search space: 2734335044
effective search space used: 2734335044
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: 53 (25.0 bits)