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= psy6338
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YFR|A Chain A, Crystal Structure Of Alanyl-Trna Synthetase In Complex
With Atp And Magnesium
pdb|1YFR|B Chain B, Crystal Structure Of Alanyl-Trna Synthetase In Complex
With Atp And Magnesium
pdb|1YFS|A Chain A, The Crystal Structure Of Alanyl-Trna Synthetase In Complex
With L-Alanine
pdb|1YFS|B Chain B, The Crystal Structure Of Alanyl-Trna Synthetase In Complex
With L-Alanine
pdb|1YFT|A Chain A, The Crystal Structure Of The Catalytic Fragment Of Alanyl-
Trna Synthetase In Complex Wtih Glycine
pdb|1YGB|A Chain A, Crystal Structure Of The Catalytic Fragment Of Alanyl-Trna
Synthetase In Complex With L-Serine
Length = 465
Score = 89.0 bits (219), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 53/136 (38%), Positives = 77/136 (56%), Gaps = 18/136 (13%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K++A A EF+T+ + LP ++LY + + DEE IW E
Sbjct: 93 MLGNFSFGDYFKKEAIEYAWEFVTEV-LKLPKEKLYVSVY--------KDDEEAYRIWNE 143
Query: 61 -LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIWN 119
+G+P + I + G + NFW+MG GPCG SSEI+ D +GE R +EIWN
Sbjct: 144 HIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVD-RGEEYEGDER-------YLEIWN 195
Query: 120 IVFISHKRVSADTIVP 135
+VF+ + R + P
Sbjct: 196 LVFMQYNRDENGVLTP 211
>pdb|3HTZ|A Chain A, Crystal Structure Of The Catalytic Fragment Of Alanyl-Trna
Synthetase In Complex With L-Serine: Re-Refined
Length = 464
Score = 89.0 bits (219), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 53/136 (38%), Positives = 77/136 (56%), Gaps = 18/136 (13%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K++A A EF+T+ + LP ++LY + + DEE IW E
Sbjct: 92 MLGNFSFGDYFKKEAIEYAWEFVTEV-LKLPKEKLYVSVY--------KDDEEAYRIWNE 142
Query: 61 -LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIWN 119
+G+P + I + G + NFW+MG GPCG SSEI+ D +GE R +EIWN
Sbjct: 143 HIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVD-RGEEYEGDER-------YLEIWN 194
Query: 120 IVFISHKRVSADTIVP 135
+VF+ + R + P
Sbjct: 195 LVFMQYNRDENGVLTP 210
>pdb|1RIQ|A Chain A, The Crystal Structure Of The Catalytic Fragment Of The
Alanyl-Trna Synthetase
Length = 465
Score = 87.8 bits (216), Expect = 2e-18, Method: Composition-based stats.
Identities = 51/135 (37%), Positives = 74/135 (54%), Gaps = 18/135 (13%)
Query: 2 LGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE- 60
LGN+SF DY+K++A A EF+T+ + LP ++LY + + DEE IW E
Sbjct: 94 LGNFSFGDYFKKEAIEYAWEFVTEV-LKLPKEKLYVSVYKD--------DEEAYRIWNEH 144
Query: 61 LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIWNI 120
+G+P + I + G + NFW+ G GPCG SSEI+ D +GE R +EIWN+
Sbjct: 145 IGIPSERIWRLGEEDNFWQXGDVGPCGPSSEIYVD-RGEEYEGDER-------YLEIWNL 196
Query: 121 VFISHKRVSADTIVP 135
VF + R + P
Sbjct: 197 VFXQYNRDENGVLTP 211
>pdb|3HXU|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Alasa
pdb|3HXV|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Glysa
pdb|3HXW|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Sersa
pdb|3HXX|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Amppcp
pdb|3HXY|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Amppcp, Ala-Amp And Pcp
Length = 441
Score = 85.1 bits (209), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 58/149 (38%), Positives = 76/149 (51%), Gaps = 26/149 (17%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPP-VSLPLDRLYFTYFGGSDQYGLPCDEETLDIW- 58
MLGN+SF DY+K DA A LT +LP +RL+ T + D+E +IW
Sbjct: 92 MLGNFSFGDYFKLDAILFAWLLLTSEKWFALPKERLWVTVY--------ESDDEAYEIWE 143
Query: 59 LELGVPRDHIKKEG-------MKCNFWEMGSTGPCGYSSEIHYDM-----KGEPSSALAR 106
E+G+PR+ I + G NFW+MG TGPCG +EI YD G P S
Sbjct: 144 KEVGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPGSP--- 200
Query: 107 VNADRNDLIEIWNIVFISHKRVSADTIVP 135
D + IEIWNIVF+ R + T+ P
Sbjct: 201 -EEDGDRYIEIWNIVFMQFNRQADGTMEP 228
>pdb|3HXZ|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|C Chain C, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|D Chain D, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HY0|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Glysa
pdb|3HY0|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Glysa
pdb|3HY1|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Sersa
pdb|3HY1|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Sersa
Length = 441
Score = 85.1 bits (209), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 58/149 (38%), Positives = 76/149 (51%), Gaps = 26/149 (17%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPP-VSLPLDRLYFTYFGGSDQYGLPCDEETLDIW- 58
MLGN+SF DY+K DA A LT +LP +RL+ T + D+E +IW
Sbjct: 92 MLGNFSFGDYFKLDAILFAWLLLTSEKWFALPKERLWVTVY--------ESDDEAYEIWE 143
Query: 59 LELGVPRDHIKKEG-------MKCNFWEMGSTGPCGYSSEIHYDM-----KGEPSSALAR 106
E+G+PR+ I + G NFW+MG TGPCG +EI YD G P S
Sbjct: 144 KEVGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPGSP--- 200
Query: 107 VNADRNDLIEIWNIVFISHKRVSADTIVP 135
D + IEIWNIVF+ R + T+ P
Sbjct: 201 -EEDGDRYIEIWNIVFMQFNRQADGTMEP 228
>pdb|4EJ3|A Chain A, Crystal Structure Of A Crispr Associated Protein From
Thermus Thermophilus Hb8
pdb|4EJ3|B Chain B, Crystal Structure Of A Crispr Associated Protein From
Thermus Thermophilus Hb8
Length = 514
Score = 29.6 bits (65), Expect = 0.53, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 20 LEFLTKPPVSLPLDRLYFTYFGGS-DQYGLPCDEE-TLDIWLE 60
LE LTK SLPL+RLY+ G+ ++ +EE +LD+W E
Sbjct: 425 LEELTKLANSLPLERLYWHALDGAFPRFFARVEEEASLDLWRE 467
>pdb|4AN8|A Chain A, Structure Of Thermus Thermophilus Casa (Cse1)
pdb|4AN8|B Chain B, Structure Of Thermus Thermophilus Casa (Cse1)
Length = 506
Score = 29.6 bits (65), Expect = 0.53, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 20 LEFLTKPPVSLPLDRLYFTYFGGS-DQYGLPCDEE-TLDIWLE 60
LE LTK SLPL+RLY+ G+ ++ +EE +LD+W E
Sbjct: 417 LEELTKLANSLPLERLYWHALDGAFPRFFARVEEEASLDLWRE 459
>pdb|4F3E|A Chain A, Crystal Structure Of Thermus Thermophilus Hb8 Casa
pdb|4F3E|B Chain B, Crystal Structure Of Thermus Thermophilus Hb8 Casa
Length = 502
Score = 29.6 bits (65), Expect = 0.53, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 20 LEFLTKPPVSLPLDRLYFTYFGGS-DQYGLPCDEE-TLDIWLE 60
LE LTK SLPL+RLY+ G+ ++ +EE +LD+W E
Sbjct: 413 LEELTKLANSLPLERLYWHALDGAFPRFFARVEEEASLDLWRE 455
>pdb|4EUT|A Chain A, Structure Of Bx-795 Complexed With Unphosphorylated Human
Tbk1 Kinase- Uld Domain
pdb|4EUT|B Chain B, Structure Of Bx-795 Complexed With Unphosphorylated Human
Tbk1 Kinase- Uld Domain
Length = 396
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 21/95 (22%)
Query: 37 FTYFGGSDQYGLPCDEETLDIWLELGVPRDHIKKEGMKCNFWEMGST------------- 83
F G+++Y P D++ + +DH KK G + W +G T
Sbjct: 172 FVSLYGTEEYLHP------DMYERAVLRKDHQKKYGATVDLWSIGVTFYHAATGSLPFRP 225
Query: 84 --GPCGYSSEIHYDMKGEPSSALARVNADRNDLIE 116
GP ++ + G+PS A++ V N I+
Sbjct: 226 FEGPRRNKEVMYKIITGKPSGAISGVQKAENGPID 260
>pdb|4EUU|A Chain A, Structure Of Bx-795 Complexed With Human Tbk1 Kinase
Domain Phosphorylated On Ser172
pdb|4EUU|B Chain B, Structure Of Bx-795 Complexed With Human Tbk1 Kinase
Domain Phosphorylated On Ser172
Length = 319
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 21/95 (22%)
Query: 37 FTYFGGSDQYGLPCDEETLDIWLELGVPRDHIKKEGMKCNFWEMGST------------- 83
F G+++Y P D++ + +DH KK G + W +G T
Sbjct: 172 FVXLYGTEEYLHP------DMYERAVLRKDHQKKYGATVDLWSIGVTFYHAATGSLPFRP 225
Query: 84 --GPCGYSSEIHYDMKGEPSSALARVNADRNDLIE 116
GP ++ + G+PS A++ V N I+
Sbjct: 226 FEGPRRNKEVMYKIITGKPSGAISGVQKAENGPID 260
>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 768
Score = 26.6 bits (57), Expect = 4.8, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 47 GLPCDEETLDIWLELGVPRDHI 68
GLP ET W++LGVP+D +
Sbjct: 549 GLPAVTET---WIKLGVPKDQL 567
>pdb|3FWL|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 751
Score = 26.6 bits (57), Expect = 5.0, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 47 GLPCDEETLDIWLELGVPRDHI 68
GLP ET W++LGVP+D +
Sbjct: 532 GLPAVTET---WIKLGVPKDQL 550
>pdb|3IZ6|A Chain A, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 305
Score = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 8/29 (27%), Positives = 19/29 (65%)
Query: 50 CDEETLDIWLELGVPRDHIKKEGMKCNFW 78
CD ++ ++++G+P ++ K+ + C FW
Sbjct: 152 CDTDSPMRYVDIGIPANNKGKQSIGCLFW 180
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
0.321 0.140 0.457
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,607,370
Number of Sequences: 62578
Number of extensions: 192007
Number of successful extensions: 405
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 383
Number of HSP's gapped (non-prelim): 19
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)