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= psy3842
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FUG|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|L Chain L, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|2FUG|U Chain U, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus
pdb|3I9V|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 2 MolASU
pdb|3I9V|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 2 MolASU
pdb|3IAM|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Reduced, 2 MolASU,
WITH BOUND NADH
pdb|3IAM|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Reduced, 2 MolASU,
WITH BOUND NADH
pdb|3IAS|3 Chain 3, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|C Chain C, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|L Chain L, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3IAS|U Chain U, Crystal Structure Of The Hydrophilic Domain Of Respiratory
Complex I From Thermus Thermophilus, Oxidized, 4 MolASU,
RE-Refined To 3.15 Angstrom Resolution
pdb|3M9S|3 Chain 3, Crystal Structure Of Respiratory Complex I From Thermus
Thermophilus
pdb|3M9S|C Chain C, Crystal Structure Of Respiratory Complex I From Thermus
Thermophilus
pdb|2YBB|3 Chain 3, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
pdb|4HEA|3 Chain 3, Crystal Structure Of The Entire Respiratory Complex I From
Thermus Thermophilus
pdb|4HEA|D Chain D, Crystal Structure Of The Entire Respiratory Complex I From
Thermus Thermophilus
Length = 783
Score = 67.0 bits (162), Expect = 3e-12, Method: Composition-based stats.
Identities = 26/49 (53%), Positives = 38/49 (77%)
Query: 3 GWRVKTNSEMTRRAREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFG 51
G V T S++ R A+ G++EF L+NHPLDCP CD+GG C+LQD+++ +G
Sbjct: 90 GMVVDTLSDVVREAQAGMVEFTLLNHPLDCPTCDKGGACELQDRTVEYG 138
Score = 59.7 bits (143), Expect = 5e-10, Method: Composition-based stats.
Identities = 21/36 (58%), Positives = 31/36 (86%)
Query: 90 AREGVMEFLLVNHPLDCPICDQGGECDLQDQSMAFG 125
A+ G++EF L+NHPLDCP CD+GG C+LQD+++ +G
Sbjct: 103 AQAGMVEFTLLNHPLDCPTCDKGGACELQDRTVEYG 138
>pdb|2FIU|A Chain A, Crystal Structure Of The Conserved Protein Of Unknown
Function Atu0297 From Agrobacterium Tumefaciens
pdb|2FIU|B Chain B, Crystal Structure Of The Conserved Protein Of Unknown
Function Atu0297 From Agrobacterium Tumefaciens
Length = 99
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 8 TNSEMTRRAREGVMEFLLVNHPLDC 32
T E T RAR V+EF V H +DC
Sbjct: 46 TELEGTARARNVVIEFPSVQHAIDC 70
>pdb|3AU2|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Complexed
With Ca-Dgtp
pdb|3AU6|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With PrimerTEMPLATE DNA AND DDGTP
pdb|3AUO|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
pdb|3AUO|B Chain B, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
Length = 575
Score = 28.1 bits (61), Expect = 1.6, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 1 MKGWRVKTNSEMTRRAREGVMEFLLVNH--PLDCPICDQGGECDLQDQSMAFGSDRSRFT 58
++ +V+ + E++R+ GV+E + V P + +G D ++ A DR T
Sbjct: 73 LRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKA-ALDRGDLT 131
Query: 59 DID-FSGKRWGYLREKLFLSELSGKR 83
+ F KR +RE L L++ +GKR
Sbjct: 132 RLKGFGPKRAERIREGLALAQAAGKR 157
>pdb|3B0X|A Chain A, K263a Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 28.1 bits (61), Expect = 1.6, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 1 MKGWRVKTNSEMTRRAREGVMEFLLVNH--PLDCPICDQGGECDLQDQSMAFGSDRSRFT 58
++ +V+ + E++R+ GV+E + V P + +G D ++ A DR T
Sbjct: 73 LRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKA-ALDRGDLT 131
Query: 59 DID-FSGKRWGYLREKLFLSELSGKR 83
+ F KR +RE L L++ +GKR
Sbjct: 132 RLKGFGPKRAERIREGLALAQAAGKR 157
>pdb|3B0Y|A Chain A, K263d Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 28.1 bits (61), Expect = 1.8, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 5 RVKTNSEMTRRAREGVMEFLLVNH--PLDCPICDQGGECDLQDQSMAFGSDRSRFTDID- 61
+V+ + E++R+ GV+E + V P + +G D ++ A DR T +
Sbjct: 77 KVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKA-ALDRGDLTRLKG 135
Query: 62 FSGKRWGYLREKLFLSELSGKR 83
F KR +RE L L++ +GKR
Sbjct: 136 FGPKRAERIREGLALAQAAGKR 157
>pdb|2D2I|A Chain A, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|B Chain B, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|O Chain O, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|P Chain P, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|Q Chain Q, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2D2I|R Chain R, Crystal Structure Of Nadp-Dependent Glyceraldehyde-3-
Phosphate Dehydrogenase From Synechococcus Sp. Complexed
With Nadp+
pdb|2DUU|A Chain A, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|B Chain B, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|O Chain O, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|P Chain P, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|Q Chain Q, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp.
pdb|2DUU|R Chain R, Crystal Structure Of Apo-Form Of Nadp-Dependent
Glyceraldehyde-3- Phosphate Dehydrogenase From
Synechococcus Sp
Length = 380
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/102 (21%), Positives = 45/102 (44%), Gaps = 7/102 (6%)
Query: 10 SEMTRRAREGVMEFLLVNHPLDCPICDQGG--ECDLQDQSMAFGSDRSRFTDIDFSGKRW 67
+E+ ++A + M+ ++ L D G E + D S+ D I + W
Sbjct: 261 NEVLQKASQTTMKGIIKYSDLPLVSSDFRGTDESSIVDSSLTLVMDGDLVKVIAWYDNEW 320
Query: 68 GYLREKLFLSELSGKRESTCAPAREGVMEFLLVNHPLDCPIC 109
GY + + L+EL+ ++ R G+++ LL++ P+
Sbjct: 321 GYSQRVVDLAELAARKS-----GRLGLVQTLLISSQDSLPLT 357
>pdb|3HYL|A Chain A, Crystal Structure Of Transketolase From Bacillus Anthracis
pdb|3HYL|B Chain B, Crystal Structure Of Transketolase From Bacillus Anthracis
pdb|3M49|A Chain A, Crystal Structure Of Transketolase Complexed With Thiamine
Diphosphate From Bacillus Anthracis
pdb|3M49|B Chain B, Crystal Structure Of Transketolase Complexed With Thiamine
Diphosphate From Bacillus Anthracis
Length = 690
Score = 26.2 bits (56), Expect = 5.7, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 38 GGECDLQDQSMAFGSDRSRFTDIDFSGKR-WGYLRE 72
GG DL + + ++ FT D+SGK W +RE
Sbjct: 401 GGSADLAGSNKTYXNNEKDFTRDDYSGKNIWYGVRE 436
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
0.322 0.139 0.440
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,141,545
Number of Sequences: 62578
Number of extensions: 154985
Number of successful extensions: 300
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 291
Number of HSP's gapped (non-prelim): 14
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
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: 46 (22.3 bits)