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= 024428
(268 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 53.9 bits (128), Expect = 9e-08, Method: Composition-based stats.
Identities = 29/61 (47%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233
G PK A W +H PYPS+E QK LA+ TGL Q+NNWFIN R+R +P
Sbjct: 3 GIFPKVATNIXRAWLFQHLTHPYPSEE-QKKQLAQDTGLTILQVNNWFINARRRIVQPXI 61
Query: 234 D 234
D
Sbjct: 62 D 62
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 53.9 bits (128), Expect = 9e-08, Method: Composition-based stats.
Identities = 25/58 (43%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
K K+G LPK A + W +H PYP+++ +K +A T L Q+NNWFIN R+R
Sbjct: 8 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKK-QIAAQTNLTLLQVNNWFINARRR 64
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
K++KG LP E+ + L DW KH YPS+E +++ L+E T L QI+NWFIN R+R
Sbjct: 8 KKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQM-LSEKTNLSLLQISNWFINARRR 64
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of
Human Homeobox Protein Tgif1, Northeast Structural
Genomics Consortium Target Hr4411b
Length = 89
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
LPKE+ Q L DW +H YPS E +K L++ T L + Q+ NWFIN R+R
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPS-EQEKALLSQQTHLSTLQVCNWFINARRR 62
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
M +RK+ K+A + L +++ H PYPS+E+++ LA+ +G+ Q++NWF N+R R
Sbjct: 1 MARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKE-ELAKKSGITVSQVSNWFGNKRIR 59
Query: 228 HWK 230
+ K
Sbjct: 60 YKK 62
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 45.1 bits (105), Expect = 4e-05, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229
+RK+ K+A + L +++ H PYPS+E+++ LA+ G+ Q++NWF N+R R+
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKE-ELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 230 K 230
K
Sbjct: 61 K 61
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 44.3 bits (103), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229
+RK+ K+A + L +++ H PYPS+E+++ LA G+ Q++NWF N+R R+
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKE-ELARKCGITVSQVSNWFGNKRIRYK 60
Query: 230 K 230
K
Sbjct: 61 K 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 43.9 bits (102), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229
+RK+ K+A + L +++ H PYPS+E+++ LA+ G+ Q++NWF N+R R+
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKE-ELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 230 K 230
K
Sbjct: 61 K 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 3/50 (6%)
Query: 178 KEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
KE + +L W H PYPS +K LAE+TGL + Q++NWF N+R+R
Sbjct: 502 KEKSRGVLREWYAHN--PYPSPR-EKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230
+ K+A + L +++ H PYPS+E+ K LA+ G+ Q++NWF N+R R+ K
Sbjct: 10 MNKQATEILNEYFYSHLSNPYPSEEA-KEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 29.6 bits (65), Expect = 1.7, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
+ KE + L W++K+ + PY + + L ++T L QI NW N+R++
Sbjct: 4 RFTKENVRILESWFAKNIENPYLDTKGLE-NLMKNTSLSRIQIKNWVSNRRRK 55
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 29.3 bits (64), Expect = 2.3, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
K + + KE + L W++K+ + PY + + L ++T L QI NW N+R++
Sbjct: 27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLE-NLMKNTSLSRIQIKNWVSNRRRK 84
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227
K + + KE + L W++K+ + PY + + L ++T L QI NW N+R++
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLE-NLMKNTSLSRIQIKNWVSNRRRK 59
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 203 KLALAESTGLDSKQINNWFINQRKRHWKPS 232
++ LAES GL Q+ W+ N+R + WK S
Sbjct: 47 RIDLAESLGLSQLQVKTWYQNRRMK-WKKS 75
>pdb|1ZS4|A Chain A, Structure Of Bacteriophage Lambda Cii Protein In Complex
With Dna
pdb|1ZS4|B Chain B, Structure Of Bacteriophage Lambda Cii Protein In Complex
With Dna
pdb|1ZS4|C Chain C, Structure Of Bacteriophage Lambda Cii Protein In Complex
With Dna
pdb|1ZS4|D Chain D, Structure Of Bacteriophage Lambda Cii Protein In Complex
With Dna
Length = 83
Score = 27.7 bits (60), Expect = 7.4, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 207 AESTGLDSKQINNWFINQRKRHWKPSEDMQFMVMD 241
AE+ G+D QI+ W KR W P M V++
Sbjct: 31 AEAVGVDKSQISRW-----KRDWIPKFSMLLAVLE 60
>pdb|1XWR|A Chain A, Crystal Structure Of The Coliphage Lambda Transcription
Activator Protein Cii
pdb|1XWR|B Chain B, Crystal Structure Of The Coliphage Lambda Transcription
Activator Protein Cii
pdb|1XWR|C Chain C, Crystal Structure Of The Coliphage Lambda Transcription
Activator Protein Cii
pdb|1XWR|D Chain D, Crystal Structure Of The Coliphage Lambda Transcription
Activator Protein Cii
pdb|1ZPQ|A Chain A, Structure Of Bacteriophage Lambda Cii Protein
pdb|1ZPQ|B Chain B, Structure Of Bacteriophage Lambda Cii Protein
pdb|1ZPQ|C Chain C, Structure Of Bacteriophage Lambda Cii Protein
pdb|1ZPQ|D Chain D, Structure Of Bacteriophage Lambda Cii Protein
Length = 97
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 207 AESTGLDSKQINNWFINQRKRHWKPSEDMQFMVMD 241
AE+ G+D QI+ W KR W P M V++
Sbjct: 30 AEAVGVDKSQISRW-----KRDWIPKFSMLLAVLE 59
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 0.131 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,292,622
Number of Sequences: 62578
Number of extensions: 263167
Number of successful extensions: 688
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 665
Number of HSP's gapped (non-prelim): 34
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)