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= psy16661
(190 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 184 bits (467), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 86/113 (76%), Positives = 96/113 (84%), Gaps = 6/113 (5%)
Query: 74 NRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKRMYIHP 133
RRMFP +KVR GLDKKAKYILLMDI+AADDCRYKFHNSRWMVAGKADPEMPKRMYIHP
Sbjct: 31 GRRMFPPFKVRCSGLDKKAKYILLMDIIAADDCRYKFHNSRWMVAGKADPEMPKRMYIHP 90
Query: 134 DSPSTGDQWMQKVVSFHKLKLTNNISDKHGFVMSASVDR------IAGSNDLL 180
DSP+TG+QWM KVV+FHKLKLTNNISDKHGF + S+ + I +ND+L
Sbjct: 91 DSPATGEQWMSKVVTFHKLKLTNNISDKHGFTILNSMHKYQPRFHIVRANDIL 143
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 27/36 (75%), Positives = 30/36 (83%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKFHN 36
MFP K R SGLD KAKYILL+DI+A+DD RYKFHN
Sbjct: 34 MFPPFKVRCSGLDKKAKYILLMDIIAADDCRYKFHN 69
>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 = 134 bits (337), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 60/99 (60%), Positives = 77/99 (77%)
Query: 74 NRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKRMYIHP 133
RRMFP+YKV+V GL+ K KYILLMDIV ADD RYKF +++W V GKA+P MP R+Y+HP
Sbjct: 32 GRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHP 91
Query: 134 DSPSTGDQWMQKVVSFHKLKLTNNISDKHGFVMSASVDR 172
DSP+TG WM+++VSF KLKLTNN D G ++ S+ +
Sbjct: 92 DSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHK 130
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 22/34 (64%), Positives = 27/34 (79%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKF 34
MFP K +V+GL+ K KYILL+DIV +DD RYKF
Sbjct: 35 MFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKF 68
>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 = 122 bits (305), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 55/101 (54%), Positives = 75/101 (74%), Gaps = 2/101 (1%)
Query: 74 NRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYK--FHNSRWMVAGKADPEMPKRMYI 131
RRMFP ++V++ G+D A Y+LLMD V DD RY+ FH+S W+VAGKADP P R++
Sbjct: 42 GRRMFPTFQVKLFGMDPMADYMLLMDFVPVDDKRYRYAFHSSSWLVAGKADPATPGRVHY 101
Query: 132 HPDSPSTGDQWMQKVVSFHKLKLTNNISDKHGFVMSASVDR 172
HPDSP+ G QWM+++VSF KLKLTNN+ D +G ++ S+ R
Sbjct: 102 HPDSPAKGAQWMKQIVSFDKLKLTNNLLDDNGHIILNSMHR 142
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDD--FRYKFHN 36
MFP + ++ G+D A Y+LL+D V DD +RY FH+
Sbjct: 45 MFPTFQVKLFGMDPMADYMLLMDFVPVDDKRYRYAFHS 82
>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 = 99.8 bits (247), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 47/116 (40%), Positives = 69/116 (59%), Gaps = 8/116 (6%)
Query: 73 HNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKRMYIH 132
+ RRMFP KV + GLD A Y +L+D VAAD+ R+K+ N W+ GK +P+ P +YIH
Sbjct: 27 NGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIH 86
Query: 133 PDSPSTGDQWMQKVVSFHKLKLTNNISDK--------HGFVMSASVDRIAGSNDLL 180
PDSP+ G WM+ VSF K+KLTN ++ H + + R+ G+ ++
Sbjct: 87 PDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNSLHKYEPRIHIVRVGGTQRMI 142
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 29/44 (65%)
Query: 1 MFPQMKFRVSGLDAKAKYILLLDIVASDDFRYKFHNRQMFPQMK 44
MFP +K +SGLD A Y +LLD VA+D+ R+K+ N + P K
Sbjct: 31 MFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGK 74
>pdb|1SDW|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase With Bound Peptide And Dioxygen
pdb|3MIB|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite
pdb|3MIC|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By
Co-Crystallization
pdb|3MID|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By Soaking
(100mm Nan3)
pdb|3MIE|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide Obtained By Soaking
(50mm Nan3)
pdb|3MIF|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Carbon Monooxide (Co)
pdb|3MIG|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite, Obtained In The
Presence Of Substrate
pdb|3MIH|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide, Obtained In The
Presence Of Substrate
pdb|3MLJ|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Carbon Monooxide (Co)
pdb|3MLK|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Nitrite
pdb|3MLL|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Azide
Length = 314
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 186 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 231
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 232 FYPVEHPVDVTFGDILAARCV 252
>pdb|4E4Z|A Chain A, Oxidized (cu2+) Peptidylglycine Alpha-hydroxylating
Monooxygenase (phm) In Complex With Hydrogen Peroxide
(1.98 A)
Length = 312
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 184 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 229
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 230 FYPVEHPVDVTFGDILAARCV 250
>pdb|1OPM|A Chain A, Oxidized (Cu2+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm) With Bound Substrate
pdb|3PHM|A Chain A, Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating
Monooxygenase (Phm)
pdb|1PHM|A Chain A, Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm)
From Rat
Length = 310
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 184 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 229
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 230 FYPVEHPVDVTFGDILAARCV 250
>pdb|1YI9|A Chain A, Crystal Structure Analysis Of The Oxidized Form Of The
M314i Mutant Of Peptidylglycine Alpha-Hydroxylating
Monooxygenase
Length = 309
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 182 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 227
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 228 FYPVEHPVDVTFGDILAARCV 248
>pdb|1YIP|A Chain A, Oxidized Peptidylglycine Alpha-hydroxylating Monooxygenase
(phm) In A New Crystal Form
Length = 311
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 184 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 229
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 230 FYPVEHPVDVTFGDILAARCV 250
>pdb|1YJL|A Chain A, Reduced Peptidylglycine Alpha-Hydroxylating Monooxygenase
In A New Crystal Form
Length = 306
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 179 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 224
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 225 FYPVEHPVDVTFGDILAARCV 245
>pdb|1YJK|A Chain A, Reduced Peptidylglycine Alpha-Hydroxylating Monooxygenase
(Phm) In A New Crystal Form
Length = 306
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 69 RYKFHNRRMFPAYKVRVMGLDKKAKYILLMDIVAADDCRYKFHNSRWMVAGKADPEMPKR 128
+YK + +F AY+V L K +V+ Y+ N +W + G+ +P++P+
Sbjct: 179 QYKMYPMHVF-AYRVHTHHLGK---------VVSG----YRVRNGQWTLIGRQNPQLPQA 224
Query: 129 MYI--HPDSPSTGDQWMQKVV 147
Y HP + GD + V
Sbjct: 225 FYPVEHPVDVTFGDILAARCV 245
>pdb|1T3T|A Chain A, Structure Of Formylglycinamide Synthetase
pdb|3UJN|A Chain A, Formyl Glycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium : Role Of The Atp Complexation
And Glutaminase Domain In Catalytic Coupling
pdb|3UMM|A Chain A, Formylglycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 27.7 bits (60), Expect = 3.9, Method: Composition-based stats.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 103 ADDCRYKFHNSRWMVAGKADPEMPKRM 129
++ CR+K N+ W++ GK P+ +M
Sbjct: 222 SEHCRHKIFNADWIIDGKPQPKSLFKM 248
>pdb|3UGJ|A Chain A, Formyl Glycinamide Ribonucletide Amidotransferase From
Salmonella Typhimurum: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 27.7 bits (60), Expect = 3.9, Method: Composition-based stats.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 103 ADDCRYKFHNSRWMVAGKADPEMPKRM 129
++ CR+K N+ W++ GK P+ +M
Sbjct: 222 SEHCRHKIFNADWIIDGKPQPKSLFKM 248
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
0.325 0.138 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,518,158
Number of Sequences: 62578
Number of extensions: 213171
Number of successful extensions: 541
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 517
Number of HSP's gapped (non-prelim): 25
length of query: 190
length of database: 14,973,337
effective HSP length: 93
effective length of query: 97
effective length of database: 9,153,583
effective search space: 887897551
effective search space used: 887897551
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)