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= 040163
(123 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZB|U Chain U, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|D Chain D, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 135
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 43 LAKHEFIQAVVLLHPSFVTVDDIEAVEVPIAVLRAEFDQISPLALLKQF 91
LA+ +F+ V +LHP+ V E E V +AE D +S QF
Sbjct: 18 LARKQFV--VDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGFRTQF 64
>pdb|1NNW|A Chain A, Hypothetical Protein From Pyrococcus Furiosus Pfu-1218608
pdb|1NNW|B Chain B, Hypothetical Protein From Pyrococcus Furiosus Pfu-1218608
Length = 252
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 72 IAVLRAEFDQISPLALLKQFEEVLTDKSEVDGYVKIFLKFS 112
+ ++R ++DQI ++ + DK E+ G+VK LKF+
Sbjct: 66 VKIIRGKYDQIIAMSDPHATDPGYIDKLELPGHVKKALKFT 106
>pdb|1XRQ|A Chain A, Crystal Structure Of Active Site F1-Mutant E245q Soaked
With Peptide Phe-Leu
pdb|1XRR|A Chain A, Crystal Structure Of Active Site F1-mutant E245q Soaked
With Peptide Pro-pro
Length = 293
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 62 VDDIEAVEVPIAVLRAEFDQISP 84
D I A+++P + E+DQ++P
Sbjct: 226 TDKISAIKIPTLITVGEYDQVTP 248
>pdb|1W61|A Chain A, Proline Racemase In Complex With 2 Molecules Of Pyrrole-2-
Carboxylic Acid (Holo Form)
pdb|1W61|B Chain B, Proline Racemase In Complex With 2 Molecules Of Pyrrole-2-
Carboxylic Acid (Holo Form)
pdb|1W62|A Chain A, Proline Racemase In Complex With One Molecule Of
Pyrrole-2- Carboxylic Acid (hemi Form)
pdb|1W62|B Chain B, Proline Racemase In Complex With One Molecule Of
Pyrrole-2- Carboxylic Acid (hemi Form)
Length = 414
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 31 VPNADRTEVAVELAKHEFIQAVVLLHPSFVTVDDIEAVEV 70
V N R + A EL + E ++V + HP ++ ++ VE+
Sbjct: 234 VQNLSRLQEAGELLRTEINRSVKVQHPQLPHINTVDCVEI 273
>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 = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 27 SRFRVPNADRTEVAVELAKHEFIQAVVLLHPS 58
SRF +P AD+T+ ++ ++ F+ VL HP+
Sbjct: 441 SRFNLPKADQTKRLLKALENPFVH--VLAHPT 470
>pdb|3B0Y|A Chain A, K263d Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 27 SRFRVPNADRTEVAVELAKHEFIQAVVLLHPS 58
SRF +P AD+T+ ++ ++ F+ VL HP+
Sbjct: 441 SRFNLPKADQTKRLLKALENPFVH--VLAHPT 470
>pdb|3B0X|A Chain A, K263a Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 27 SRFRVPNADRTEVAVELAKHEFIQAVVLLHPS 58
SRF +P AD+T+ ++ ++ F+ VL HP+
Sbjct: 441 SRFNLPKADQTKRLLKALENPFVH--VLAHPT 470
>pdb|4B0R|A Chain A, Structure Of The Deamidase-Depupylase Dop Of The
Prokaryotic Ubiquitin-Like Modification Pathway
pdb|4B0S|A Chain A, Structure Of The Deamidase-depupylase Dop Of The
Prokaryotic Ubiquitin-like Modification Pathway In
Complex With Atp
Length = 506
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 5 TLIKDYIQALDPVWAQPEKIWISRFRVPNADRTEVAVELAKHEFIQAVVLLHPSFVTVDD 64
TL + I D A PEK + +A+ +E+A L + ++ F++ D
Sbjct: 218 TLKRPIINTRDEPHADPEKYRRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQD- 276
Query: 65 IEAVEVPIAVLRA 77
+VE P+ LRA
Sbjct: 277 -FSVESPVGALRA 288
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
0.323 0.138 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,495,293
Number of Sequences: 62578
Number of extensions: 118416
Number of successful extensions: 345
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 342
Number of HSP's gapped (non-prelim): 8
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)