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= psy3393
(433 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 167 bits (422), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 76/81 (93%), Positives = 79/81 (97%)
Query: 352 LEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR 411
+EEINTKE+AQRI+ ELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR
Sbjct: 1 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR 60
Query: 412 RMWKWLQEPEFQRMSALRLAG 432
RMWKWLQEPEFQRMSALRLA
Sbjct: 61 RMWKWLQEPEFQRMSALRLAA 81
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 164 bits (415), Expect = 8e-41, Method: Compositional matrix adjust.
Identities = 75/79 (94%), Positives = 77/79 (97%)
Query: 354 EINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRM 413
EINTKE+AQRI+ ELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRM
Sbjct: 1 EINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRM 60
Query: 414 WKWLQEPEFQRMSALRLAG 432
WKWLQEPEFQRMSALRLA
Sbjct: 61 WKWLQEPEFQRMSALRLAA 79
>pdb|1WH6|A Chain A, Solution Structure Of The Second Cut Domain Of Human
Homeobox Protein Cux-2
Length = 101
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 36/77 (46%), Positives = 51/77 (66%), Gaps = 6/77 (7%)
Query: 347 GNSGELE-----EINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWS 401
G+SG+ E E++T EL +++ +L + I Q IF ++VL SQG++SD+L PKPWS
Sbjct: 4 GSSGQYELYMYREVDTLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWS 63
Query: 402 KL-KSGRETFRRMWKWL 417
KL + GRE F RM WL
Sbjct: 64 KLTQKGREPFIRMQLWL 80
>pdb|1WH8|A Chain A, Solution Structure Of The Third Cut Domain Of Human
Homeobox Protein Cux-2
Length = 111
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/68 (41%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 354 EINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRR 412
E++T + +R+ L ++ Q +F + +L +QG++SDLL PKPW KL GRE F R
Sbjct: 26 ELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVR 85
Query: 413 MWKWLQEP 420
M WL +P
Sbjct: 86 MQLWLNDP 93
>pdb|1X2L|A Chain A, Solution Structure Of The Cut Domain Of Human Homeobox
Protein Cux-2 (Cut-Like 2)
Length = 101
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 52/80 (65%), Gaps = 3/80 (3%)
Query: 351 ELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRET 409
E E+++T E+A ++ +L +++I Q +F VL SQG++S++L PKPW KL G+E
Sbjct: 13 EEEQLDTAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEP 72
Query: 410 FRRMWKWLQEPEFQRMSALR 429
F +M ++L + Q + ALR
Sbjct: 73 FIKMKQFLSDE--QNVLALR 90
>pdb|1WIZ|A Chain A, Solution Structure Of The First Cut Domain Of Kiaa1034
Protein
Length = 101
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 6/86 (6%)
Query: 345 SLGNSGELEEINTK-----ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK- 398
S G+SG+ E N+ ++ Q++ ELKR S+ QA+FA+ R+QG LS++LR +
Sbjct: 2 SSGSSGKPEPTNSSVEVSPDIYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEED 61
Query: 399 PWSKLKSGRETFRRMWKWLQEPEFQR 424
P + +S R M +L PE +R
Sbjct: 62 PRTASQSLLVNLRAMQNFLNLPEVER 87
>pdb|1YSE|A Chain A, Solution Structure Of The Mar-Binding Domain Of Satb1
Length = 141
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKLKSGRETFRRMWKWL 417
E+ Q + ELKR I QA+FA+ R+QG LS++LR + P + +S R M +L
Sbjct: 25 EIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFL 84
Query: 418 QEPEFQR 424
Q PE +R
Sbjct: 85 QLPEAER 91
>pdb|2O49|A Chain A, Crystal Structure Of The N-Terminal Cut Domain Of Satb1
Bound To Matrix Attachment Region Dna
pdb|2O4A|A Chain A, Crystal Structure Of The N-Terminal Cut Domain Of Satb1
Bound To Matrix Attachment Region Dna
Length = 93
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKLKSGRETFRRMWKWL 417
E+ Q + ELKR I QA+FA+ R+QG LS++LR + P + +S R M +L
Sbjct: 11 EIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFL 70
Query: 418 QEPEFQR 424
Q PE +R
Sbjct: 71 QLPEAER 77
>pdb|2CSF|A Chain A, Solution Structure Of The Second Cut Domain Of Human Satb2
Length = 101
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 36/76 (47%), Gaps = 15/76 (19%)
Query: 357 TKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLR---NPKP-----WSKLKSGRE 408
T + I E+KR + QA+FA+ +SQG L +LLR NP P W L
Sbjct: 19 TAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLC---- 74
Query: 409 TFRRMWKWLQEPEFQR 424
T RR L P+ +R
Sbjct: 75 TIRRF---LNLPQHER 87
>pdb|2YO0|A Chain A, Salmonella Enterica Sada 1049-1304 Fused To Gcn4 Adaptors
(Sadak9-Cfi)
pdb|2YO1|A Chain A, Salmonella Enterica Sada 1049-1304 Fused To Gcn4 Adaptors
(Sadak9-Cfii)
pdb|2YO1|B Chain B, Salmonella Enterica Sada 1049-1304 Fused To Gcn4 Adaptors
(Sadak9-Cfii)
pdb|2YO1|C Chain C, Salmonella Enterica Sada 1049-1304 Fused To Gcn4 Adaptors
(Sadak9-Cfii)
Length = 322
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 62/145 (42%), Gaps = 7/145 (4%)
Query: 133 TLTPLQPLPPISTMSDKFAYGHTGNVTGSFTVMQNN--IGLGINSHYTYDKIQ-MSPPQH 189
T TP + ST D A G G+ T++ + IG+G+N+ D I ++ +
Sbjct: 37 TTTPTKYYHANSTEEDSLAVGTDSLAMGAKTIVNADAGIGIGLNTLVMADAINGIAIGSN 96
Query: 190 YSPNNGLSTIVITQENSPLSPQSTYSQNGLNSPQKSLSPNSYDSPYNQRDLVDRSVLGGG 249
N+ S + + Q+ Y+ +++PQ S+ S S QR + + + G
Sbjct: 97 ARANHANSIAMGNGSQTTRGAQTDYTAYNMDTPQNSVGEFSVGSEDGQRQITN---VAAG 153
Query: 250 SQSPTLSPNEGSLHSSPTTLVTNFQ 274
S + T + N G L + + N Q
Sbjct: 154 S-ADTDAVNVGQLKVTDAQVSRNTQ 177
>pdb|2EX2|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli
pdb|2EX6|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli, Complexed With Ampicillin
pdb|2EX8|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli, Complexed With Penicillin-G
pdb|2EX9|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli, Complexed With Penicillin-V
pdb|2EXA|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli, Complexed With Farom
pdb|2EXB|A Chain A, Crystal Structure Of Penicillin Binding Protein 4 (Dacb)
From Escherichia Coli, Complexed With Flomox
Length = 458
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 290 PHTVVVSPQTSPQHSLISNQLQRSDS 315
P TVV S Q++P H L+ L++SD+
Sbjct: 264 PGTVVASKQSAPLHDLLKIMLKKSDN 289
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
0.310 0.126 0.357
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,209,723
Number of Sequences: 62578
Number of extensions: 479049
Number of successful extensions: 634
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 621
Number of HSP's gapped (non-prelim): 16
length of query: 433
length of database: 14,973,337
effective HSP length: 102
effective length of query: 331
effective length of database: 8,590,381
effective search space: 2843416111
effective search space used: 2843416111
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (25.0 bits)