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= 019947
(333 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 = 62.4 bits (150), Expect = 4e-10, Method: Composition-based stats.
Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
+G P T++ +AW H PYP+EE K +L Q+TGL + Q+NNWFIN R+R
Sbjct: 2 SGIFPKVATNIXRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 55
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 40/63 (63%)
Query: 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318
K + G LP T+++++W H PYPTE++K ++ +T L L Q+NNWFIN R+R
Sbjct: 8 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 67
Query: 319 ANP 321
+ P
Sbjct: 68 SGP 70
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
K+R G LP ++ +L+ W H YP+EE+K L ++T L L QI+NWFIN R+R
Sbjct: 8 KKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRR 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 = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 32/51 (62%)
Query: 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
LP ++ +L+ W H YP+E++KA L Q+T L Q+ NWFIN R+R
Sbjct: 12 LPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
RKRR T +L ++ SH PYP+EE K L +++G+ + Q++NWF N+R R
Sbjct: 4 RKRR--NFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIR 59
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 48.5 bits (114), Expect = 5e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
RKRR T +L ++ SH PYP+EE K L ++ G+ + Q++NWF N+R R
Sbjct: 3 RKRR--NFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 48.1 bits (113), Expect = 7e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
RKRR T +L ++ SH PYP+EE K L ++ G+ + Q++NWF N+R R
Sbjct: 3 RKRR--NFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 58
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
RKRR + +L ++ SH PYP+EE K L ++ G+ + Q++NWF N+R R
Sbjct: 3 RKRR--NFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIR 58
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 30/46 (65%)
Query: 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
T +L ++ SH PYP+EE K L ++ G+ + Q++NWF N+R R
Sbjct: 15 TEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 277 WLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 316
W +H PYP+ +K L + TGL Q++NWF N+R+R+
Sbjct: 512 WYAHN--PYPSPREKRELAEATGLTTTQVSNWFKNRRQRD 549
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 273 LKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
L+A S A+ P P +E+ RL ET + ++I++WF +RK+
Sbjct: 19 LRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|3PM0|A Chain A, Structural Characterization Of The Complex Between Alpha-
Naphthoflavone And Human Cytochrome P450 1b1 (Cyp1b1)
Length = 507
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 265 LPGDTTSLLKAWWLSH--AKWPYPTEEDKARLVQETGLQLKQINN 307
+P DT + W ++H KWP P D AR + + GL K + +
Sbjct: 374 IPKDTVVFVNQWSVNHDPLKWPNPENFDPARFLDKDGLINKDLTS 418
>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 = 31.6 bits (70), Expect = 0.57, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 32/65 (49%)
Query: 251 DIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFI 310
D+ + + R + + +L++W+ + + PY + L++ T L QI NW
Sbjct: 20 DMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVS 79
Query: 311 NQRKR 315
N+R++
Sbjct: 80 NRRRK 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 = 31.6 bits (70), Expect = 0.61, Method: Composition-based stats.
Identities = 14/55 (25%), Positives = 28/55 (50%)
Query: 261 RAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
R + + +L++W+ + + PY + L++ T L QI NW N+R++
Sbjct: 5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 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 = 31.2 bits (69), Expect = 0.75, Method: Composition-based stats.
Identities = 14/55 (25%), Positives = 28/55 (50%)
Query: 261 RAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
R + + +L++W+ + + PY + L++ T L QI NW N+R++
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 55
>pdb|1G69|A Chain A, Thiamin Phosphate Synthase
pdb|1G69|B Chain B, Thiamin Phosphate Synthase
Length = 228
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 136 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 179
>pdb|1G4E|A Chain A, Thiamin Phosphate Synthase
pdb|1G4E|B Chain B, Thiamin Phosphate Synthase
pdb|1G6C|A Chain A, Thiamin Phosphate Synthase
pdb|1G6C|B Chain B, Thiamin Phosphate Synthase
Length = 227
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 135 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 178
>pdb|1G4P|A Chain A, Thiamin Phosphate Synthase
pdb|1G4P|B Chain B, Thiamin Phosphate Synthase
pdb|1G4S|A Chain A, Thiamin Phosphate Synthase
pdb|1G4S|B Chain B, Thiamin Phosphate Synthase
Length = 226
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 134 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 177
>pdb|2TPS|A Chain A, Thiamin Phosphate Synthase
pdb|2TPS|B Chain B, Thiamin Phosphate Synthase
pdb|1G4T|A Chain A, Thiamin Phosphate Synthase
pdb|1G4T|B Chain B, Thiamin Phosphate Synthase
Length = 227
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 135 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 178
>pdb|1G67|A Chain A, Thiamin Phosphate Synthase
pdb|1G67|B Chain B, Thiamin Phosphate Synthase
Length = 225
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 133 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 176
>pdb|3O15|A Chain A, Crystal Structure Of Bacillus Subtilis Thiamin Phosphate
Synthase Complexed With A Carboxylated Thiazole
Phosphate
Length = 235
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+++ SL+E VR +QG IV I
Sbjct: 143 DGADYVGLGPIYPTETKKDTRAVQGVSLIEAVR-------RQGISIPIVGI 186
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 279 SHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314
S K +PT+ + RL ET L ++I++WF +RK
Sbjct: 31 SFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRK 66
>pdb|3O16|A Chain A, Crystal Structure Of Bacillus Subtilis Thiamin Phosphate
Synthase K159a
Length = 235
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 15/51 (29%)
Query: 210 DGPDSMGFGPLVPTESER--------SLMERVRHELKHELKQGYKEKIVDI 252
DG D +G GP+ PTE+ + SL+E VR +QG IV I
Sbjct: 143 DGADYVGLGPIYPTETAKDTRAVQGVSLIEAVR-------RQGISIPIVGI 186
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 23/31 (74%)
Query: 286 PTEEDKARLVQETGLQLKQINNWFINQRKRN 316
P++E + + Q+ GL+L ++N+F+N R+R+
Sbjct: 122 PSKELQITISQQLGLELSTVSNFFMNARRRS 152
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 282 KWPYPTEEDKARLVQETGLQLKQINNWFINQR 313
+WP P E DK L +E+GL I +WF + R
Sbjct: 48 QWPSPEEYDK--LAKESGLARTDIVSWFGDTR 77
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 28.1 bits (61), Expect = 6.6, Method: Composition-based stats.
Identities = 13/55 (23%), Positives = 26/55 (47%)
Query: 261 RAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315
R + + +L++W+ + + PY + L++ T L QI NW +R +
Sbjct: 5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAK 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 = 28.1 bits (61), Expect = 8.1, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 285 YPTEEDKARLVQETGLQLKQINNWFINQRKR 315
+P + + RL++ TGL +I WF + R R
Sbjct: 28 FPDDAEVYRLIEVTGLARSEIKKWFSDHRYR 58
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
0.318 0.132 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,618,212
Number of Sequences: 62578
Number of extensions: 337635
Number of successful extensions: 1043
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1019
Number of HSP's gapped (non-prelim): 38
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
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: 52 (24.6 bits)