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= 027250
(226 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DA6|A Chain A, Solution Structure Of The Homeobox Domain Of Hepatocyte
Nuclear Factor 1-Beta (Hnf-1beta)
Length = 102
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 18/80 (22%)
Query: 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAK-------------H 132
GS + R R+ PA QIL YD K P K++ + + E + H
Sbjct: 1 GSSGSSGRNRFKWGPASQQILYQAYDRQK-NPSKEEREALVEECNRAECLQRGVSPSKAH 59
Query: 133 GQ----ISETNVYNWFQNRR 148
G ++E VYNWF NRR
Sbjct: 60 GLGSNLVTEVRVYNWFANRR 79
>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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 127 AELAKHGQISETNVYNWFQNRRARLKRKQ 155
A LAK+ +++ET V WFQNRR + KRKQ
Sbjct: 35 AHLAKNLKLTETQVKIWFQNRRYKTKRKQ 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 = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 150
R R T + +QL LE ++ + + D+ ELA+ ++E + WFQNRRAR
Sbjct: 20 RSRTTFSASQLDELERAFE-------RTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR 72
Query: 151 LKRKQSGV 158
L+++ + V
Sbjct: 73 LRKQHTSV 80
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 75 GNPYFDPFVA-SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHG 133
N F P++A +G+ L R R T T Q LE + R+++I E+A
Sbjct: 3 SNHTFYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRI-----EMAHAL 57
Query: 134 QISETNVYNWFQNRRARLKR 153
++E + WFQNRR +LK+
Sbjct: 58 SLTERQIKIWFQNRRMKLKK 77
>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 = 34.7 bits (78), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 12/78 (15%)
Query: 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNW 143
GSQ+ RQR T QLQ LE T ++ + DM+ E+A ++E V W
Sbjct: 1 GSQR---RQRTHFTSQQLQELE-------ATFQRNRYPDMSTREEIAVWTNLTEARVRVW 50
Query: 144 FQNRRARLKRKQSGVVPN 161
F+NRRA+ ++++ +V +
Sbjct: 51 FKNRRAKWRKREEFIVTD 68
>pdb|2H8R|A Chain A, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
pdb|2H8R|B Chain B, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
Length = 221
Score = 33.5 bits (75), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 46/112 (41%), Gaps = 24/112 (21%)
Query: 54 EQLVQMHKVFSAQNEIAGMRMGNPYFDPFVASGSQKLTARQRWTPTPAQLQILEHVYDEC 113
+QL+ + FS Q+ G D + + K R R+ PA QIL YD
Sbjct: 111 DQLLFLFPEFSQQSHGPGQS------DDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQ 164
Query: 114 KGTPRKQKIQDMTAELAK-------------HGQ----ISETNVYNWFQNRR 148
K P K++ + + E + HG ++E VYNWF NRR
Sbjct: 165 K-NPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR 215
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 33.5 bits (75), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 18/25 (72%)
Query: 129 LAKHGQISETNVYNWFQNRRARLKR 153
LAK Q+SE V WFQNRRA+ +R
Sbjct: 40 LAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 33.5 bits (75), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNW 143
GSQ+ RQR T QLQ LE T ++ DM+ E+A ++E V W
Sbjct: 1 GSQR---RQRTHFTSQQLQELE-------ATFQRNHYPDMSTREEIAVWTNLTEARVRVW 50
Query: 144 FQNRRARLKRKQSGVVPN 161
F+NRRA+ ++++ +V +
Sbjct: 51 FKNRRAKWRKREEFIVTD 68
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQD--MTAELAKHGQISETNVYNWFQNRRAR 150
R+R T T AQL +LE ++ K + D M E+A + E+ V WF+NRRA+
Sbjct: 9 RERTTFTRAQLDVLEALFA-------KTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
Query: 151 LK 152
+
Sbjct: 62 CR 63
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 32.3 bits (72), Expect = 0.25, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 23/33 (69%)
Query: 127 AELAKHGQISETNVYNWFQNRRARLKRKQSGVV 159
+++A ++SE V WFQNRRA+ KR ++G V
Sbjct: 38 SQIAHALKLSEVQVKIWFQNRRAKWKRIKAGNV 70
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 32.0 bits (71), Expect = 0.28, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152
R R T QL+ LE+++ E K + Q LA+ + E V WF+NRRA+ +
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQ-----LARKVHLREEKVEVWFKNRRAKWR 63
Query: 153 R 153
R
Sbjct: 64 R 64
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 107 EHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 154
E + + C IQ +L+ +++ VYNWF NRR +KR+
Sbjct: 38 EEIANACNAV-----IQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR 80
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 7/62 (11%)
Query: 93 RQRWTPTPAQLQILEHVYD-ECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151
R R T Q+++LE+V+ C D+ +LA+ + + WFQNRRA+L
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGI------DILEDLAQKLNLELDRIQIWFQNRRAKL 56
Query: 152 KR 153
KR
Sbjct: 57 KR 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 = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 150
R R T T QL+ LE V+ K D+ A +LA ++E V WFQNRRA+
Sbjct: 11 RNRTTFTSYQLEELEKVFQ-------KTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
Query: 151 LKRKQ 155
++++
Sbjct: 64 WRKRE 68
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 150
R R T T QL+ LE ++ + D+ ELA+ +++E V WF NRRAR
Sbjct: 4 RSRTTFTAEQLEELERAFE-------RTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
Query: 151 LKRKQS 156
RKQ+
Sbjct: 57 W-RKQA 61
>pdb|1KVD|B Chain B, Killer Toxin From Halotolerant Yeast
pdb|1KVD|D Chain D, Killer Toxin From Halotolerant Yeast
pdb|1KVE|B Chain B, Killer Toxin From Halotolerant Yeast
pdb|1KVE|D Chain D, Killer Toxin From Halotolerant Yeast
Length = 77
Score = 30.4 bits (67), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 114 KGTPRKQKIQDMTAELAKHG 133
KGTP K +Q+M+A+LAK+G
Sbjct: 17 KGTPSKNDLQNMSADLAKNG 36
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.4 bits (67), Expect = 0.90, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 93 RQRWTP-TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 151
R+ TP T AQL LE + + + ++ AE + ++ET V WFQNRRA+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAER-----AEFSSSLSLTETQVKIWFQNRRAKA 55
Query: 152 KR 153
KR
Sbjct: 56 KR 57
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 155
T QL LE + K R +++ E+A +++ET V WFQNRR + K+++
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRV-----EIAATLELNETQVKIWFQNRRMKQKKRE 93
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
++ ELAK I+ + V NWF N+R R K+
Sbjct: 32 EEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>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 = 29.3 bits (64), Expect = 1.6, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 152
R R T AQL LE + K R +++ ELA ++E ++ WFQNRR + K
Sbjct: 5 RTRTAYTRAQLLELEKEFLFNKYISRPRRV-----ELAVMLNLTERHIKIWFQNRRMKWK 59
Query: 153 RKQ 155
+++
Sbjct: 60 KEE 62
>pdb|1LFB|A Chain A, The X-Ray Structure Of An Atypical Homeodomain Present In
The Rat Liver Transcription Factor Lfb1(Slash)hnf1 And
Implications For Dna Binding
Length = 99
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 135
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 11 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 69
Query: 136 SETNVYNWFQNRR 148
+E VYNWF NRR
Sbjct: 70 TEVRVYNWFANRR 82
>pdb|2LFB|A Chain A, Homeodomain From Rat Liver Lfb1HNF1 TRANSCRIPTION FACTOR,
Nmr, 20 Structures
Length = 100
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 135
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 12 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 70
Query: 136 SETNVYNWFQNRR 148
+E VYNWF NRR
Sbjct: 71 TEVRVYNWFANRR 83
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 127 AELAKHGQISETNVYNWFQNRRARLKR 153
A LAK ++++ V WFQNRR + +R
Sbjct: 28 AALAKALRMTDAQVKTWFQNRRTKWRR 54
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 6/35 (17%)
Query: 116 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150
+PR+++ ELA+ ++ T V NWF+NRR R
Sbjct: 520 SPREKR------ELAEATGLTTTQVSNWFKNRRQR 548
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 28.9 bits (63), Expect = 2.3, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 118 RKQKIQDMT----AELAKHGQISETNVYNWFQNRRARLKR 153
R QK Q + AELA +++T V WFQN+R+++K+
Sbjct: 25 RFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150
R R T TP QL+IL Y RK M +A + + V WFQN RAR
Sbjct: 19 RLRTTITPEQLEILYQKYLLDSNPTRK-----MLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|1IC8|A Chain A, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
pdb|1IC8|B Chain B, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
Length = 194
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 93 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 135
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 117 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 175
Query: 136 SETNVYNWFQNRR 148
+E VYNWF NRR
Sbjct: 176 TEVRVYNWFANRR 188
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.9 bits (63), Expect = 2.7, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
++ ELAK I+ + V NWF N+R R K+
Sbjct: 33 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
++ ELAK I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.5 bits (62), Expect = 3.1, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 87 SQKLTARQRWTP-TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145
S L R++ P T QL+ LE Y K +D ++ +SE V WFQ
Sbjct: 2 SHMLEGRKKRVPYTKVQLKELEREY-----ATNKFITKDKRRRISATTNLSERQVTIWFQ 56
Query: 146 NRRARLKR 153
NRR + K+
Sbjct: 57 NRRVKEKK 64
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 28.5 bits (62), Expect = 3.6, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 86 GSQKLTARQRWTP-TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 144
GS + R++ P + QL+ LE Y K +D +++ +SE + WF
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREY-----AANKFITKDKRRKISAATSLSERQITIWF 55
Query: 145 QNRRARLKRKQSG 157
QNRR +K K+SG
Sbjct: 56 QNRR--VKEKKSG 66
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 28.1 bits (61), Expect = 3.7, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
++ ELAK I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
+D E+A+ ++E V WFQNRR ++K+
Sbjct: 28 RDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153
+ QL L+ ++E + +++ Q +++EL ++E + WFQN+RA++K+
Sbjct: 11 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNKRAKIKK 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 128 ELAKHGQISETNVYNWFQNRRARLKRKQSGV 158
ELA ++E + WFQNRRA+ RKQ V
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKW-RKQEKV 60
>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 = 27.7 bits (60), Expect = 6.0, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
++ ELA+ I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>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 = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 127 AELAKHGQISETNVYNWFQNRRARLKR 153
A LA+ ++++ V WFQNRR + +R
Sbjct: 48 AALARGLKMTDAQVKTWFQNRRTKWRR 74
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 99 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 153
+ QL L+ ++E + +++ Q +++EL ++E + WFQN+RA++K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNKRAKIKK 58
>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 = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 128 ELAKHGQISETNVYNWFQNRRARLKRKQSGV 158
ELA ++E + WFQNRRA+ RKQ V
Sbjct: 38 ELAMKIGLTEARIQVWFQNRRAKW-RKQEKV 67
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 123 QDMTAELAKHGQISETNVYNWFQNRRARLKR 153
+D E+A+ ++E V WFQNRR ++K+
Sbjct: 40 RDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>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 = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150
T RQR + T Q LE + + R+++I E+A ++E + WFQNRR +
Sbjct: 28 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRI-----EIAHALSLTERQIKIWFQNRRMK 82
Query: 151 LKR 153
K+
Sbjct: 83 WKK 85
>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 = 26.9 bits (58), Expect = 8.5, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 91 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 150
+ R R T T Q LE + + R+++I ++A +SE + WFQNRR +
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRI-----DIANALSLSERQIKIWFQNRRMK 57
Query: 151 LKRKQS 156
K+ ++
Sbjct: 58 SKKDRT 63
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 128 ELAKHGQISETNVYNWFQNRRARLKRKQ 155
ELA ++E + WFQNRRA+ ++++
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 86 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 145
G+ + ++R T + A LE + E P Q+I M EL ++ V WF
Sbjct: 82 GANERKRKRRTTISIAAKDALERHFGE-HSKPSSQEIMRMAEELNLEKEV----VRVWFC 136
Query: 146 NRRARLKR 153
NRR R KR
Sbjct: 137 NRRQREKR 144
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 0.130 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,786,922
Number of Sequences: 62578
Number of extensions: 257346
Number of successful extensions: 695
Number of sequences better than 100.0: 61
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 655
Number of HSP's gapped (non-prelim): 61
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)