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= 005518
(693 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 = 72.0 bits (175), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 43/59 (72%)
Query: 368 LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426
P+ + ++ RAWLF+H HPYP + K+ LA+ TGLT QV+NWFINAR R+ +P +++
Sbjct: 5 FPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQ 63
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 30/56 (53%), Positives = 43/56 (76%), Gaps = 1/56 (1%)
Query: 365 QRG-LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRL 419
+RG LP+ + +V+R+WLF+H HPYP + +K+ +A QT LT QV+NWFINAR R+
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 66.2 bits (160), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 368 LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426
LP SV +LR W+++H YP + +KQML+++T L+ 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 = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 41/59 (69%)
Query: 368 LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426
LP+ SV +LR WL+EH + YP + +K +L++QT L+ QV NWFINAR RL M+ +
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK 70
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 39/61 (63%)
Query: 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420
A R +R +++ +L + + H +PYP + K+ LAK++G+T SQVSNWF N R+R
Sbjct: 2 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 421 K 421
K
Sbjct: 62 K 62
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 55.5 bits (132), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 366 RGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421
R + +++ +L + + H +PYP + K+ LAK+ G+T SQVSNWF N R+R K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 55.5 bits (132), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420
A R +R +++ +L + + H +PYP + K+ LAK+ G+T SQVSNWF N R+R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 421 K 421
K
Sbjct: 61 K 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 38/61 (62%)
Query: 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420
A R +R +++ +L + + H +PYP + K+ LAK+ G+T SQVSNWF N R+R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 421 K 421
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 = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLW 420
A R +R +++ +L + + H +PYP + K+ LA++ G+T SQVSNWF N R+R
Sbjct: 1 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 421 K 421
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 = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/49 (53%), Positives = 33/49 (67%), Gaps = 3/49 (6%)
Query: 370 ERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVR 418
E+S VLR W + H +PYP +K+ LA+ TGLT +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 = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 363 RPQRG--LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416
+P RG + +V +L +W ++ +PY + L K T L+R Q+ NW N R
Sbjct: 27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 82
>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 = 36.6 bits (83), Expect = 0.054, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 363 RPQRG--LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416
+P RG + +V +L +W ++ +PY + L K T L+R 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 = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 363 RPQRG--LPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVR 418
+P RG + +V +L +W ++ +PY + L K T L+R Q+ NW R +
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 59
>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 = 33.9 bits (76), Expect = 0.29, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 370 ERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416
+ +V +L +W ++ +PY + L K T L+R Q+ NW N R
Sbjct: 7 KENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53
>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 = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 393 DKQMLAKQTGLTRSQVSNWFINARVR 418
+K+ +AK+ G+T QV WFIN R+R
Sbjct: 394 EKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 389 PKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMVEE 426
P D + LA++TGLT+ + WF NAR + + ++ +
Sbjct: 32 PDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ 69
>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 = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 388 YPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWKPMV 424
+P D++ L + TGL RS++ WF + R R + +V
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 377 RAWLFEHFLHPYPKDS-DKQMLAKQTGLTRSQVSNWFINARVR 418
RA+L E F +S +K+ +AK+ G+T QV WFIN R+R
Sbjct: 17 RAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 387 PYPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421
P P++ DK LAK++GL R+ + +WF + R WK
Sbjct: 50 PSPEEYDK--LAKESGLARTDIVSWFGDTRYA-WK 81
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 361 AWRPQRGLPERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINAR 416
A + + L E VS L+ + +P DS+ L K TGLT+ ++ WF + R
Sbjct: 11 AKKTKEQLAELKVSYLK--------NQFPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
>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 = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 370 ERSVSVLRAWLFEHFLHPYPKDSDKQMLAKQTGLTRSQVSNWFINARVRL 419
ER+ LRA +P P D + L +T +TR ++ +WF R ++
Sbjct: 13 ERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>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 = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 388 YPKDSDKQMLAKQTGLTRSQVSNWFINARVRLWK 421
YP ++ LA++T LT +++ WF N R RL K
Sbjct: 42 YPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 377 RAWLFEHFLHPYPKDS-DKQMLAKQTGLTRSQVSNWFINARVR 418
RA+L + F +S +K+ +AK+ G+T QV WFIN R+R
Sbjct: 9 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 377 RAWLFEHFLHPYPKDS-DKQMLAKQTGLTRSQVSNWFINARVR 418
RA+L + F +S +K+ +AK+ G+T QV WFIN R+R
Sbjct: 17 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 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 = 28.9 bits (63), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 388 YPKDSDKQMLAKQTGLTRSQVSNWFINARVRL 419
Y + +Q L+ + GL +Q+ WF NAR ++
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNARAKI 56
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
0.314 0.129 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,431,098
Number of Sequences: 62578
Number of extensions: 582218
Number of successful extensions: 946
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 919
Number of HSP's gapped (non-prelim): 28
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)