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= 009253
(539 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
Length = 249
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/132 (31%), Positives = 58/132 (43%), Gaps = 23/132 (17%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
+++ L Y GT + GLQ R L T++GELE AL G L K A
Sbjct: 2 RRLLLLCEYDGTLFAGLQ--RQGRGLRTVQGELERAL--------PGIGALPKAVAA--G 49
Query: 138 RTDKGVHSLATMICLKME--IPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFD 195
RTD GVH+LA + +E IP + + + +N LP ++KV F
Sbjct: 50 RTDAGVHALAMPFHVDVESAIPVE---------KVPEALNRLLPEDLKVVGAREVAPDFH 100
Query: 196 PRRECNLRKYSY 207
R++ R Y Y
Sbjct: 101 ARKDALWRAYRY 112
Score = 28.5 bits (62), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 384 VEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSL-AKHSRIVLPLAPSEVLFL 440
V + G+SF+ Q+R MVGT + V P + L L R+ P AP+ L+
Sbjct: 184 VRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYF 241
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
Length = 270
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 70/165 (42%), Gaps = 27/165 (16%)
Query: 68 SDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGN 127
SD + PV K+AL + Y G+ Y G Q Q + + +++ +LE AL +
Sbjct: 2 SDQQQPPV--YKIALGIEYDGSKYYGWQRQNE---VRSVQEKLEKALSQVAN-------- 48
Query: 128 LQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSI 187
+ I + RTD GVH ++ + KD + + VNA+LP +I V +
Sbjct: 49 -EPITVFCAGRTDAGVHGTGQVVHFETTA---LRKDAAWTLG----VNANLPGDIAVRWV 100
Query: 188 LPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDF 232
F R R+Y Y++ N +L A + ++ F
Sbjct: 101 KTVPDDFHARFSATARRYRYII------YNHRLRPAVLSKGVTHF 139
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 383 YVEISISGESFMLHQIRKMVGTAVAVKRKLLPRD-ILTLSLAKHSRIVLPLAPSEVLFLR 441
YV + I +F+ H +R +VG+ + V P I L AK + A +E L+L
Sbjct: 189 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 248
Query: 442 ANSFSVR 448
A + R
Sbjct: 249 AVDYPDR 255
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
Length = 264
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/154 (24%), Positives = 65/154 (42%), Gaps = 25/154 (16%)
Query: 79 KVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSR 138
K+AL + Y G+ Y G Q Q + + +++ +LE AL + + I + R
Sbjct: 5 KIALGIEYDGSKYYGWQRQNE---VRSVQEKLEKALSQVAN---------EPITVFCAGR 52
Query: 139 TDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRR 198
TD GVH ++ + KD + + VNA+LP +I V + F R
Sbjct: 53 TDAGVHGTGQVVHFETTA---LRKDAAWTLG----VNANLPGDIAVRWVKTVPDDFHARF 105
Query: 199 ECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDF 232
R+Y Y++ N +L A + ++ F
Sbjct: 106 SATARRYRYII------YNHRLRPAVLSKGVTHF 133
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 383 YVEISISGESFMLHQIRKMVGTAVAVKRKLLPRD-ILTLSLAKHSRIVLPLAPSEVLFLR 441
YV + I +F+ H +R +VG+ + V P I L AK + A +E L+L
Sbjct: 183 YVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLV 242
Query: 442 ANSFSVR 448
A + R
Sbjct: 243 AVDYPDR 249
>pdb|1IRU|F Chain F, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
pdb|1IRU|T Chain T, Crystal Structure Of The Mammalian 20s Proteasome At 2.75
A Resolution
Length = 263
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 16/98 (16%)
Query: 143 VHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNL 202
V L ++I K +IP + PYG+ L + + +F PS FD R
Sbjct: 105 VSRLVSLIGSKTQIPTQRYGRRPYGVGLL--IAGYDDMGPHIFQTCPSANYFDCR----- 157
Query: 203 RKYSYLLPAEVIGINSQLTAAEIDSHISDF-NAILNEF 239
A IG SQ ++ H+S+F LNE
Sbjct: 158 --------AMSIGARSQSARTYLERHMSEFMECNLNEL 187
>pdb|3ZEN|D Chain D, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|E Chain E, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|3ZEN|F Chain F, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|A Chain A, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|B Chain B, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
pdb|4B3Y|C Chain C, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
Length = 3089
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 58 HTLTRPTPNSSDDKWEPVRKKKVALRV 84
HT+ RP P+SSD WE RK +RV
Sbjct: 2587 HTVARPLPDSSD--WEVTRKAGTEIRV 2611
>pdb|3UNB|E Chain E, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|S Chain S, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|GG Chain g, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNB|UU Chain u, Mouse Constitutive 20s Proteasome In Complex With Pr-957
pdb|3UNE|E Chain E, Mouse Constitutive 20s Proteasome
pdb|3UNE|S Chain S, Mouse Constitutive 20s Proteasome
pdb|3UNE|GG Chain g, Mouse Constitutive 20s Proteasome
pdb|3UNE|UU Chain u, Mouse Constitutive 20s Proteasome
pdb|3UNF|E Chain E, Mouse 20s Immunoproteasome In Complex With Pr-957
pdb|3UNF|S Chain S, Mouse 20s Immunoproteasome In Complex With Pr-957
pdb|3UNH|E Chain E, Mouse 20s Immunoproteasome
pdb|3UNH|S Chain S, Mouse 20s Immunoproteasome
Length = 263
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 15/90 (16%)
Query: 143 VHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNL 202
V L ++I K +IP + PYG+ L + + +F PS FD R
Sbjct: 105 VSRLVSLIGSKTQIPTQRYGRRPYGVGLL--IAGYDDMGPHIFQTCPSANYFDCR----- 157
Query: 203 RKYSYLLPAEVIGINSQLTAAEIDSHISDF 232
A IG SQ ++ H+S+F
Sbjct: 158 --------AMSIGARSQSARTYLERHMSEF 179
>pdb|2TAA|A Chain A, Structure And Possible Catalytic Residues Of Taka-Amylase
A
pdb|2TAA|B Chain B, Structure And Possible Catalytic Residues Of Taka-Amylase
A
pdb|2TAA|C Chain C, Structure And Possible Catalytic Residues Of Taka-Amylase
A
Length = 478
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 477 SVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVR 516
+V+LP++ D K+ W +W+ +L SI ++D V+
Sbjct: 170 TVSLPDLDTTKDVVKNEWYDWVGSLVSNYSIDGLRIDTVK 209
>pdb|2GUY|A Chain A, Orthorhombic Crystal Structure (Space Group P21212) Of
Aspergillus Niger Alpha-Amylase At 1.6 A Resolution
pdb|2GVY|A Chain A, Monoclinic Crystal Form Of Aspergillus Niger Alpha-Amylase
In Complex With Maltose At 1.8 A Resolution
pdb|2GVY|B Chain B, Monoclinic Crystal Form Of Aspergillus Niger Alpha-Amylase
In Complex With Maltose At 1.8 A Resolution
pdb|6TAA|A Chain A, Structure And Molecular Model Refinement Of Aspergillus
Oryzae (Taka) Alpha-Amylase: An Application Of The
Simulated-Annealing Method
pdb|7TAA|A Chain A, Family 13 Alpha Amylase In Complex With Acarbose
pdb|3KWX|A Chain A, Chemically Modified Taka Alpha-Amylase
Length = 478
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 477 SVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRN 517
+V+LP++ D K+ W +W+ +L SI ++D V++
Sbjct: 170 TVSLPDLDTTKDVVKNEWYDWVGSLVSNYSIDGLRIDTVKH 210
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
0.316 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,698,062
Number of Sequences: 62578
Number of extensions: 563839
Number of successful extensions: 1407
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1394
Number of HSP's gapped (non-prelim): 15
length of query: 539
length of database: 14,973,337
effective HSP length: 104
effective length of query: 435
effective length of database: 8,465,225
effective search space: 3682372875
effective search space used: 3682372875
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: 54 (25.4 bits)