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= 048159
(840 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 70.9 bits (172), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 30/56 (53%), Positives = 42/56 (75%), Gaps = 1/56 (1%)
Query: 627 QRG-LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRV 681
+RG LP+ A ++R+WLF+H HPYPT+ +K +A QT L+ QV+NWFINAR R+
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 70.5 bits (171), Expect = 4e-12, Method: Composition-based stats.
Identities = 30/59 (50%), Positives = 41/59 (69%)
Query: 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688
P+ A I RAWLF+H HPYP++ K LA TGL+ QV+NWFINAR R+ +P +++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQ 63
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 66.6 bits (161), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 41/59 (69%)
Query: 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688
LP +V ILR W+++H YP++ +K ML+ +T LS Q+SNWFINAR R+ M+++
Sbjct: 14 LPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ 72
>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 = 63.9 bits (154), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 41/59 (69%)
Query: 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688
LP+ +V ILR WL+EH + YP++ +K +L+ QT LS QV NWFINAR R+ M+ +
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK 70
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
R + ++A IL + + H +PYP++ K LA + G++ +QVSNWF N R+R K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
R +R ++A IL + + H +PYP++ K LA ++G++ +QVSNWF N R+R K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
R +R ++A IL + + H +PYP++ K LA + G++ +QVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 50.4 bits (119), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
R +R ++A IL + + H +PYP++ K LA + G++ +QVSNWF N R+R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 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 = 50.1 bits (118), Expect = 5e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
R +R ++A IL + + H +PYP++ K LA + G++ +QVSNWF N R+R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 632 ERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVR 680
E++ +LR W + H +PYP+ +K LA TGL+ QVSNWF N R R
Sbjct: 503 EKSRGVLREW-YAH--NPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 602 QILQKHKSGGANVGFLEPQQHV---WRPQRG--LPERAVAILRAWLFEHFLHPYPTDTDK 656
Q+ QK+KS V + Q + +P RG + V IL +W ++ +PY
Sbjct: 1 QLTQKNKSADGLVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGL 60
Query: 657 HMLATQTGLSRNQVSNWFINAR 678
L T LSR Q+ NW N R
Sbjct: 61 ENLMKNTSLSRIQIKNWVSNRR 82
>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 = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 632 ERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRV 681
ERA LRA +P P D + L ++T ++R ++ +WF R +V
Sbjct: 13 ERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>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 = 33.5 bits (75), Expect = 0.46, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 625 RPQRG--LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINAR 678
+P RG + V IL +W ++ +PY L T LSR Q+ NW N R
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 57
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 625 RPQRG--LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVR 680
+P RG + V IL +W ++ +PY L T LSR Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 59
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 650 YPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686
+P D + + L TGL+R+++ WF + R R + +V
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 31.2 bits (69), Expect = 2.8, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 21/44 (47%)
Query: 635 VAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINAR 678
V IL +W ++ +PY L T LSR Q+ NW N R
Sbjct: 10 VRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>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 = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 650 YPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683
Y T+ + L+++ GL+ QV WF N R ++ K
Sbjct: 28 YLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
Length = 217
Score = 30.4 bits (67), Expect = 4.5, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 161 ESNQNVMLDGEVVSNNSNSTSRKILRPNNYNEYQDHVQSTSVNQPSEKLFGDMHYATP 218
E+ + + EVV +++T+R +L+P +Q V ++ P + GD YA+P
Sbjct: 128 ETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHXLALGHP---ILGDRFYASP 182
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
0.313 0.127 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,419,131
Number of Sequences: 62578
Number of extensions: 859325
Number of successful extensions: 1483
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1464
Number of HSP's gapped (non-prelim): 23
length of query: 840
length of database: 14,973,337
effective HSP length: 107
effective length of query: 733
effective length of database: 8,277,491
effective search space: 6067400903
effective search space used: 6067400903
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: 56 (26.2 bits)