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= 022553
(295 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 87.8 bits (216), Expect = 7e-18, Method: Composition-based stats.
Identities = 40/57 (70%), Positives = 46/57 (80%), Gaps = 1/57 (1%)
Query: 106 YRGVRMRPWGKWAAEIRDPFQR-TRVWLGTFETAEEAALVYDQAAIRLKGPHAQTNF 161
YRGVR RPWGK+AAEIRDP + RVWLGTFETAE+AAL YD+AA R++G A NF
Sbjct: 3 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr, 46
Structures
Length = 70
Score = 87.8 bits (216), Expect = 7e-18, Method: Composition-based stats.
Identities = 40/57 (70%), Positives = 46/57 (80%), Gaps = 1/57 (1%)
Query: 106 YRGVRMRPWGKWAAEIRDPFQR-TRVWLGTFETAEEAALVYDQAAIRLKGPHAQTNF 161
YRGVR RPWGK+AAEIRDP + RVWLGTFETAE+AAL YD+AA R++G A NF
Sbjct: 6 YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62
>pdb|3EZ2|A Chain A, Partition Protein-Adp Complex
pdb|3EZ2|B Chain B, Partition Protein-Adp Complex
pdb|3EZ6|A Chain A, Structure Of Para-Adp Complex:tetragonal Form
pdb|3EZ6|B Chain B, Structure Of Para-Adp Complex:tetragonal Form
Length = 398
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 55/133 (41%), Gaps = 22/133 (16%)
Query: 160 NFLRPPQTDQTFDFVTSGYDSEKESQSQTPTSAI---PSPTSVLRFHSNEEIELAKTELF 216
N + ++D F V SG + ++ ++ I P P + + FHS+ + EL
Sbjct: 236 NVIDKLKSDYDFILVDSGPHLDAFLKNALASANILFTPLPPATVDFHSSLKYVARLPELV 295
Query: 217 NLESDRCCPSQDSFQI-YDSELLDSATPAPIFFDDKMCVPLLKENLGDVSVDL------- 268
L SD C Q + I + S+L + A D K C L KE G +D+
Sbjct: 296 KLISDEGCECQLATNIGFMSKLSNKA-------DHKYCHSLAKEVFGGDMLDVFLPRLDG 348
Query: 269 ----GGDFDSCIS 277
G FD+ IS
Sbjct: 349 FERCGESFDTVIS 361
>pdb|1WH8|A Chain A, Solution Structure Of The Third Cut Domain Of Human
Homeobox Protein Cux-2
Length = 111
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 77 SCSESVKQRMKDRSIPLKKRVGGRSYDNKYRGV------RMRPWGKWAAEIRDPFQRTRV 130
S ++ VK+ + D + L +R+ G S +G R +PW K + + R+PF R ++
Sbjct: 31 SITKRVKEVLTDNN--LGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQL 88
Query: 131 WL 132
WL
Sbjct: 89 WL 90
>pdb|3EZ7|A Chain A, Partition Protein Apo Form In Space Group I4122
Length = 398
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 55/133 (41%), Gaps = 22/133 (16%)
Query: 160 NFLRPPQTDQTFDFVTSGYDSEKESQSQTPTSAI---PSPTSVLRFHSNEEIELAKTELF 216
N + ++D F V SG + ++ ++ I P P + + FHS+ + EL
Sbjct: 236 NVIDKLKSDYDFILVDSGPHLDAFLKNALASANILFTPLPPATVDFHSSLKYVARLPELV 295
Query: 217 NLESDRCCPSQDSFQI-YDSELLDSATPAPIFFDDKMCVPLLKENLGDVSVDL------- 268
L SD C Q + I + S+L + A D K C L KE G +D+
Sbjct: 296 KLISDEGCECQLATNIGFMSKLSNKA-------DHKYCHSLAKEVFGGDMLDVFLPRLDG 348
Query: 269 ----GGDFDSCIS 277
G FD+ IS
Sbjct: 349 FERCGESFDTVIS 361
>pdb|2YG5|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c Mutant
Length = 453
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 5/114 (4%)
Query: 64 EIRIVECSKSNEISCSESVKQRMKDRSIPLKKRVGGRSYDNKYRGVRMRPWGKWAAEIRD 123
++ IV S + + K + I + RVGGR++ + G + G+W + +
Sbjct: 7 DVAIVGAGPSGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQT 66
Query: 124 PFQRTRVWLG--TFETAEEAALVYDQAA---IRLKGPHAQTNFLRPPQTDQTFD 172
LG TFE E VY +A R G TN + D+ D
Sbjct: 67 ALISLLDELGLKTFERYREGESVYISSAGERTRYTGDSFPTNETTKKEMDRLID 120
>pdb|2YG7|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
pdb|2YG7|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: A394c-A396t-Q431g Triple Mutant
Length = 453
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 5/114 (4%)
Query: 64 EIRIVECSKSNEISCSESVKQRMKDRSIPLKKRVGGRSYDNKYRGVRMRPWGKWAAEIRD 123
++ IV S + + K + I + RVGGR++ + G + G+W + +
Sbjct: 7 DVAIVGAGPSGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQT 66
Query: 124 PFQRTRVWLG--TFETAEEAALVYDQAA---IRLKGPHAQTNFLRPPQTDQTFD 172
LG TFE E VY +A R G TN + D+ D
Sbjct: 67 ALISLLDELGLKTFERYREGESVYISSAGERTRYTGDSFPTNETTKKEMDRLID 120
>pdb|2YG6|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
pdb|2YG6|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: P15i-A394c Double Mutant
Length = 453
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 5/114 (4%)
Query: 64 EIRIVECSKSNEISCSESVKQRMKDRSIPLKKRVGGRSYDNKYRGVRMRPWGKWAAEIRD 123
++ IV S + + K + I + RVGGR++ + G + G+W + +
Sbjct: 7 DVAIVGAGISGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQT 66
Query: 124 PFQRTRVWLG--TFETAEEAALVYDQAA---IRLKGPHAQTNFLRPPQTDQTFD 172
LG TFE E VY +A R G TN + D+ D
Sbjct: 67 ALISLLDELGLKTFERYREGESVYISSAGERTRYTGDSFPTNETTKKEMDRLID 120
>pdb|2YG3|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG3|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Enzyme
pdb|2YG4|A Chain A, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
pdb|2YG4|B Chain B, Structure-Based Redesign Of Cofactor Binding In Putrescine
Oxidase: Wild Type Bound To Putrescine
Length = 453
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 44/114 (38%), Gaps = 5/114 (4%)
Query: 64 EIRIVECSKSNEISCSESVKQRMKDRSIPLKKRVGGRSYDNKYRGVRMRPWGKWAAEIRD 123
++ IV S + + K + I + RVGGR++ + G + G+W + +
Sbjct: 7 DVAIVGAGPSGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQT 66
Query: 124 PFQRTRVWLG--TFETAEEAALVYDQAA---IRLKGPHAQTNFLRPPQTDQTFD 172
LG TFE E VY +A R G TN + D+ D
Sbjct: 67 ALISLLDELGLKTFERYREGESVYISSAGERTRYTGDSFPTNETTKKEMDRLID 120
>pdb|1WH6|A Chain A, Solution Structure Of The Second Cut Domain Of Human
Homeobox Protein Cux-2
Length = 101
Score = 27.7 bits (60), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 110 RMRPWGKWAAEIRDPFQRTRVWL 132
R +PW K + R+PF R ++WL
Sbjct: 58 RPKPWSKLTQKGREPFIRMQLWL 80
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
0.315 0.131 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,000,292
Number of Sequences: 62578
Number of extensions: 300309
Number of successful extensions: 529
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 12
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)