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= psy434
(307 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A04|A Chain A, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
pdb|4A04|B Chain B, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
Length = 203
Score = 202 bits (515), Expect = 2e-52, Method: Compositional matrix adjust.
Identities = 95/122 (77%), Positives = 104/122 (85%), Gaps = 1/122 (0%)
Query: 131 SSSWVVAGKADPISPPRIHVHPDSPASGAQWSKQVVSFDKLKLTNNQLDDNGHIILNSMH 190
SSSW+VAGKADP +P R+H HPDSPA GAQW KQ+VSFDKLKLTNN LDDNGHIILNSMH
Sbjct: 82 SSSWLVAGKADPATPGRVHYHPDSPAKGAQWMKQIVSFDKLKLTNNLLDDNGHIILNSMH 141
Query: 191 KYQPRFHVVLLSPESNSAS-ATSPFKTFLFPETMFTAVTAYQNHRITQLKIASNPFAKGF 249
+YQPRFHVV + P +S A FKTF+F ET FTAVTAYQNHRITQLKIASNPFAKGF
Sbjct: 142 RYQPRFHVVYVDPRKDSEKYAEENFKTFVFEETRFTAVTAYQNHRITQLKIASNPFAKGF 201
Query: 250 RE 251
R+
Sbjct: 202 RD 203
>pdb|2X6U|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Free Form
pdb|2X6V|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
pdb|2X6V|B Chain B, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
Length = 203
Score = 166 bits (421), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 79/135 (58%), Positives = 96/135 (71%), Gaps = 2/135 (1%)
Query: 131 SSSWVVAGKADPISPPRIHVHPDSPASGAQWSKQVVSFDKLKLTNNQLDDNGHIILNSMH 190
+ W V GKA+P P R++VHPDSPA+GA W +Q+VSF KLKLTNN LD GHIILNSMH
Sbjct: 70 DNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMH 129
Query: 191 KYQPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHRITQLKIASNPFAKGFR 250
KYQPR H+V + S + F T +FPET F AVT+YQNH+ITQLKI +NPFAKGFR
Sbjct: 130 KYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFR 189
Query: 251 ECEPDDCSAETLNQM 265
DD +++M
Sbjct: 190 GS--DDMELHRMSRM 202
>pdb|1H6F|A Chain A, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
pdb|1H6F|B Chain B, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
Length = 193
Score = 156 bits (395), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 76/122 (62%), Positives = 93/122 (76%), Gaps = 2/122 (1%)
Query: 131 SSSWVVAGKADPISPPRIHVHPDSPASGAQWSKQVVSFDKLKLTNNQLDDNGHIILNSMH 190
+S W+VAGKADP P R+++HPDSPA+G QW +VV+F KLKLTNN D +G ILNSMH
Sbjct: 69 NSRWMVAGKADPEMPKRMYIHPDSPATGEQWMSKVVTFHKLKLTNNISDKHGFTILNSMH 128
Query: 191 KYQPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHRITQLKIASNPFAKGFR 250
KYQPRFH+V + +T F+T+LFPET F AVTAYQN +ITQLKI +NPFAKGFR
Sbjct: 129 KYQPRFHIVRANDILKLPYST--FRTYLFPETEFIAVTAYQNDKITQLKIDNNPFAKGFR 186
Query: 251 EC 252
+
Sbjct: 187 DT 188
>pdb|1XBR|A Chain A, T Domain From Xenopus Laevis Bound To Dna
pdb|1XBR|B Chain B, T Domain From Xenopus Laevis Bound To Dna
Length = 184
Score = 118 bits (295), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 59/123 (47%), Positives = 78/123 (63%), Gaps = 7/123 (5%)
Query: 131 SSSWVVAGKADPISPPRIHVHPDSPASGAQWSKQVVSFDKLKLTNNQLDDNGHIILNSMH 190
+ WV GK +P +P +++HPDSP GA W K VSF K+KLT N+++ G I+LNS+H
Sbjct: 66 NGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLT-NKMNGGGQIMLNSLH 124
Query: 191 KYQPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHRITQLKIASNPFAKGFR 250
KY+PR H+V + ++ S FPET F AVTAYQN IT LKI NPFAK F
Sbjct: 125 KYEPRIHIVRVGGTQRMITSHS------FPETQFIAVTAYQNEEITALKIKHNPFAKAFL 178
Query: 251 ECE 253
+ +
Sbjct: 179 DAK 181
>pdb|2GP4|A Chain A, Structure Of [fes]cluster-free Apo Form Of
6-phosphogluconate Dehydratase From Shewanella
Oneidensis
pdb|2GP4|B Chain B, Structure Of [fes]cluster-free Apo Form Of
6-phosphogluconate Dehydratase From Shewanella
Oneidensis
Length = 628
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 221 ETMFTAVTAYQNHRITQLKIASNPFAKGFRECEPDDCSA 259
E A+ +NH + + ++ A GF C PDD +A
Sbjct: 41 EAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNA 79
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
0.321 0.135 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,271,958
Number of Sequences: 62578
Number of extensions: 310985
Number of successful extensions: 559
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 550
Number of HSP's gapped (non-prelim): 6
length of query: 307
length of database: 14,973,337
effective HSP length: 99
effective length of query: 208
effective length of database: 8,778,115
effective search space: 1825847920
effective search space used: 1825847920
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)