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= psy488
(86 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Y96|B Chain B, Crystal Structure Of The Gemin6GEMIN7 HETERODIMER FROM
THE Human Smn Complex
pdb|1Y96|D Chain D, Crystal Structure Of The Gemin6GEMIN7 HETERODIMER FROM
THE Human Smn Complex
Length = 85
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 16 AEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHAL 75
A +RE++L+++ ++ G + + E V A F T+ D+ FYV L+TPIG E AL
Sbjct: 14 AALRERYLRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQTPIGVQAE-AL 72
Query: 76 LRVDDIVD 83
LR DI+
Sbjct: 73 LRCSDIIS 80
>pdb|2V6Z|M Chain M, Solution Structure Of Amino Terminal Domain Of Human Dna
Polymerase Epsilon Subunit B
Length = 99
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 17 EMREKFLKAMSSLSGQPCTINMFERTVVTAEFQ 49
E+ +K K ++++ QP + NM ER+VV A Q
Sbjct: 64 ELEDKLEKIINAVEKQPLSSNMIERSVVEAAVQ 96
>pdb|1PRT|C Chain C, The Crystal Structure Of Pertussis Toxin
pdb|1PRT|I Chain I, The Crystal Structure Of Pertussis Toxin
pdb|1PTO|C Chain C, The Structure Of A Pertussis Toxin-Sugar Complex As A
Model For Receptor Binding
pdb|1PTO|I Chain I, The Structure Of A Pertussis Toxin-Sugar Complex As A
Model For Receptor Binding
Length = 196
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 27/65 (41%)
Query: 19 REKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRV 78
RE F +GQP + + + T TNS L +VR+ ++ IG R
Sbjct: 80 RETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRY 139
Query: 79 DDIVD 83
D+ D
Sbjct: 140 RDMYD 144
>pdb|1BCP|C Chain C, Binary Complex Of Pertussis Toxin And Atp
pdb|1BCP|I Chain I, Binary Complex Of Pertussis Toxin And Atp
Length = 199
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 27/65 (41%)
Query: 19 REKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRV 78
RE F +GQP + + + T TNS L +VR+ ++ IG R
Sbjct: 83 RETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRY 142
Query: 79 DDIVD 83
D+ D
Sbjct: 143 RDMYD 147
>pdb|1OHF|A Chain A, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|B Chain B, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|C Chain C, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|D Chain D, The Refined Structure Of Nudaurelia Capensis Omega Virus
Length = 644
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 42 TVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIV 82
++VT +QG V N+ TP G F LL+ D+I+
Sbjct: 517 SIVTKTYQGWEG------VTNVNTPFGQFAHSGLLKNDEIL 551
>pdb|1PRT|B Chain B, The Crystal Structure Of Pertussis Toxin
pdb|1PRT|H Chain H, The Crystal Structure Of Pertussis Toxin
pdb|1PTO|B Chain B, The Structure Of A Pertussis Toxin-Sugar Complex As A
Model For Receptor Binding
Length = 196
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 15 AAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68
A +++ F + +GQP T + + T TNS L +VR+ + IG
Sbjct: 76 AFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIG 129
>pdb|1ZYZ|A Chain A, Structures Of Yeast Ribonucloetide Reductase I
pdb|1ZYZ|B Chain B, Structures Of Yeast Ribonucloetide Reductase I
pdb|1ZZD|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVS|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVT|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVU|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVV|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVW|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVX|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2CVY|A Chain A, Structures Of Yeast Ribonucleotide Reductase I
pdb|2EUD|A Chain A, Structures Of Yeast Ribonucleotide Reductase I Complexed
With Ligands And Subunit Peptides
pdb|2ZLF|A Chain A, The Structural Basis For Peptidomimetic Inhibition Of
Eukaryotic Ribonucleotide Reductase
pdb|2ZLG|A Chain A, The Structual Basis For Peptidomimetic Inhibition Of
Eukaryotic Ribonucleotide Reductase
pdb|3K8T|A Chain A, Structure Of Eukaryotic Rnr Large Subunit R1 Complexed
With Designed Adp Analog Compound
pdb|3PAW|A Chain A, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|B Chain B, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|C Chain C, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3PAW|D Chain D, Low Resolution X-Ray Crystal Structure Of Yeast Rnr1p With
Datp Bound In The A-Site
pdb|3S87|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 With Dgtp
And Adp
pdb|3S8B|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 With Amppnp
And Cdp
pdb|3RSR|A Chain A, Crystal Structure Of 5-Nitp Inhibition Of Yeast
Ribonucleotide Reductase
Length = 888
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 32 QPCTINMFERTVVTAEFQGTN 52
+P T NM+ R V++ EFQ N
Sbjct: 622 EPVTSNMYSRRVLSGEFQVVN 642
>pdb|3S8A|A Chain A, Structure Of Yeast Ribonucleotide Reductase R293a With
Dgtp
pdb|3S8C|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 R293a With
Amppnp And Cdp
Length = 888
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 32 QPCTINMFERTVVTAEFQGTN 52
+P T NM+ R V++ EFQ N
Sbjct: 622 EPVTSNMYSRRVLSGEFQVVN 642
>pdb|3TB9|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 Q288a With
Amppnp And Cdp
pdb|3TBA|A Chain A, Structure Of Yeast Ribonucleotide Reductase 1 Q288a With
Dgtp And Adp
Length = 888
Score = 26.6 bits (57), Expect = 3.7, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 32 QPCTINMFERTVVTAEFQGTN 52
+P T NM+ R V++ EFQ N
Sbjct: 622 EPVTSNMYSRRVLSGEFQVVN 642
>pdb|1PTO|H Chain H, The Structure Of A Pertussis Toxin-Sugar Complex As A
Model For Receptor Binding
Length = 198
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 15 AAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68
A +++ F + +GQP T + + T TNS L +VR+ + IG
Sbjct: 78 AFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIG 131
>pdb|1BCP|B Chain B, Binary Complex Of Pertussis Toxin And Atp
pdb|1BCP|H Chain H, Binary Complex Of Pertussis Toxin And Atp
Length = 199
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 15 AAEMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTPIG 68
A +++ F + +GQP T + + T TNS L +VR+ + IG
Sbjct: 79 AFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIG 132
>pdb|2W2D|A Chain A, Crystal Structure Of A Catalytically Active, Non-Toxic
Endopeptidase Derivative Of Clostridium Botulinum Toxin
A
pdb|2W2D|C Chain C, Crystal Structure Of A Catalytically Active, Non-Toxic
Endopeptidase Derivative Of Clostridium Botulinum Toxin
A
Length = 450
Score = 26.6 bits (57), Expect = 4.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 42 TVVTAEFQGTNSDLTEFYVRNLKTPIGTFHEHALLRVDDIV 82
T + A F G N+++ LK G F + LL VD I+
Sbjct: 399 TNLAANFNGQNTEINNMNFTKLKNFTGLFEFYKLLCVDGII 439
>pdb|4E9L|A Chain A, Fdec, A Novel Broadly Conserved Escherichia Coli Adhesin
Eliciting Protection Against Urinary Tract Infections
Length = 420
Score = 26.2 bits (56), Expect = 5.2, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 23 LKAMSSLSGQPCTINMFERTVVTAEFQGTNSDLTEFYVRNLKTP 66
L+ M +GQP + TV+ E NS L V + KTP
Sbjct: 269 LRVMPLFNGQPAATEAAQLTVIAGEMSSANSTL----VADNKTP 308
>pdb|2VDW|A Chain A, Guanosine N7 Methyl-Transferase Sub-Complex (D1-D12) Of
The Vaccinia Virus Mrna Capping Enzyme
pdb|2VDW|C Chain C, Guanosine N7 Methyl-Transferase Sub-Complex (D1-D12) Of
The Vaccinia Virus Mrna Capping Enzyme
pdb|2VDW|E Chain E, Guanosine N7 Methyl-Transferase Sub-Complex (D1-D12) Of
The Vaccinia Virus Mrna Capping Enzyme
pdb|2VDW|G Chain G, Guanosine N7 Methyl-Transferase Sub-Complex (D1-D12) Of
The Vaccinia Virus Mrna Capping Enzyme
Length = 302
Score = 25.4 bits (54), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 17 EMREKFLKAMSSLSGQPCTINMFERTVVTAEFQGTN-SDLTEFYV 60
E +KF+ S++ +P T N FE + +G + DL +YV
Sbjct: 251 ERSKKFINGASTMEDRPSTRNFFELNRGAIKCEGLDVEDLLSYYV 295
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 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,192,438
Number of Sequences: 62578
Number of extensions: 68459
Number of successful extensions: 220
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 208
Number of HSP's gapped (non-prelim): 15
length of query: 86
length of database: 14,973,337
effective HSP length: 54
effective length of query: 32
effective length of database: 11,594,125
effective search space: 371012000
effective search space used: 371012000
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: 45 (21.9 bits)