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= psy6028
(141 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|BB Chain b, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 147
Score = 78.2 bits (191), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 4/140 (2%)
Query: 2 VSSHLIWNIVKNNNAYLMKA---DNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTA 58
V LIW IVK NN +L+K N K F+KEP NL N+ S+K+SGL + KT+ IQP+
Sbjct: 4 VPEPLIWEIVKKNNCFLVKQFGNSNAKVQFTKEPNNLYNVHSYKHSGLANKKTVTIQPSG 63
Query: 59 DNKGFACVTKRATKKYK-PGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAALRRA 117
++ TKK P K K + R+ ++ + N YR +LTK AL R
Sbjct: 64 VKDAAVVLSTTKTKKQNAPAKLYHKSVMRKEFRKMAKAVKNQVSDNYYRPDLTKPALARL 123
Query: 118 SAVLQSQKRAQIPAKKSNKK 137
S+V +S + ++ AKK N++
Sbjct: 124 SSVYRSLQVSKSGAKKKNRQ 143
>pdb|4A18|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|O Chain O, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 134
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 62/138 (44%), Gaps = 10/138 (7%)
Query: 4 SHLIWNIVKNNNAYLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGF 63
S L+W IVKNNNA+L+K + + F+ +P ++ + G H + ++ A
Sbjct: 2 SQLVWEIVKNNNAFLVKNNGVA--FTTDPFSVTGRNTQVGLGFTHRHGVALKGGAKQAIA 59
Query: 64 ACVTKRATKKYKPGKAVIKQEW---KSGPRRSLLKLRKYIVGNKYRKELTKAALRRASAV 120
+ K + K K I+ E K G +R + K I G K L + AL++
Sbjct: 60 TSLRKNQSHKVKK-TGTIEAETLTVKGGVQR----VAKVIRGRFQSKGLKQFALKKLVNF 114
Query: 121 LQSQKRAQIPAKKSNKKK 138
++ RAQ K +K K
Sbjct: 115 HRANVRAQANLKAESKAK 132
>pdb|2Q3B|A Chain A, 1.8 A Resolution Crystal Structure Of O-Acetylserine
Sulfhydrylase (Oass) Holoenzyme From Mycobacterium
Tuberculosis
pdb|2Q3C|A Chain A, 2.1 A Resolution Crystal Structure Of O-Acetylserine
Sulfhydrylase (Oass) Holoenzyme From Mycobacterium
Tuberculosis In Complex With The Inhibitory Peptide Dfsi
Length = 313
Score = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 38 LASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKYKPGKAVIKQEWKSGPRRSLLK 95
L + + +GLI TI ++PT+ N G A A + Y+ + E S RR LL+
Sbjct: 55 LQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYR--CVLTMPETMSLERRMLLR 110
>pdb|4I1Y|A Chain A, The Structure Of Cysteine Synthase From Mycobacterium
Ulcerans Agy99
pdb|4I1Y|B Chain B, The Structure Of Cysteine Synthase From Mycobacterium
Ulcerans Agy99
pdb|4I1Y|C Chain C, The Structure Of Cysteine Synthase From Mycobacterium
Ulcerans Agy99
pdb|4I1Y|D Chain D, The Structure Of Cysteine Synthase From Mycobacterium
Ulcerans Agy99
Length = 314
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 44 SGLIHSKTIHIQPTADNKGFACVTKRATKKYKPGKAVIKQEWKSGPRRSLLKLRKYIVGN 103
+GLI TI ++PT+ N G A A + YK + + S RR LL+
Sbjct: 62 AGLIKPDTIILEPTSGNTGIALAMVSAARGYK--CVLTMPDTMSIERRMLLR-------- 111
Query: 104 KYRKE--LTKAALRRASAVLQSQKRAQ 128
Y E LT A A A+ ++++ A+
Sbjct: 112 AYGAELVLTPGAEGMAGAIAKAEELAK 138
>pdb|3RR2|A Chain A, Structure Of A Cysteine Synthase (O-Acetylserine
Sulfhydrylase (Oass)) From Mycobacterium Marinum Atcc
Baa-535 M
Length = 314
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 44 SGLIHSKTIHIQPTADNKGFACVTKRATKKYKPGKAVIKQEWKSGPRRSLLKLRKYIVGN 103
+GLI TI ++PT+ N G A A + YK + + S RR LL+
Sbjct: 62 AGLIKPDTIILEPTSGNTGIALAMVSAARGYK--CVLTMPDTMSIERRMLLR-------- 111
Query: 104 KYRKE--LTKAALRRASAVLQSQKRAQ 128
Y E LT A A A+ ++++ A+
Sbjct: 112 AYGAELVLTPGAEGMAGAIAKAEELAK 138
>pdb|2Q3D|A Chain A, 2.2 A Resolution Crystal Structure Of O-acetylserine
Sulfhydrylase (oass) From Mycobacterium Tuberculosis In
Complex With The Reaction Intermediate
Alpha-aminoacrylate
Length = 313
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 38 LASFKYSGLIHSKTIHIQPTADNKGFACVTKRATKKYKPGKAVIKQEWKSGPRRSLLK 95
L + + +GLI TI ++PT+ N G A A + Y+ + E S RR LL+
Sbjct: 55 LQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYR--CVLTMPETMSLERRMLLR 110
>pdb|3BJS|A Chain A, Crystal Structure Of A Member Of Enolase Superfamily From
Polaromonas Sp. Js666
pdb|3BJS|B Chain B, Crystal Structure Of A Member Of Enolase Superfamily From
Polaromonas Sp. Js666
Length = 428
Score = 27.3 bits (59), Expect = 2.7, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 35 LPNLASFKYSGLIHSKTIHIQPTADNKGF--ACVTK 68
+P A +GL H+ TIH +N G+ ACV+K
Sbjct: 333 IPINAHSSATGLNHAATIHFLAATENAGYFEACVSK 368
>pdb|3GB8|A Chain A, Crystal Structure Of Crm1SNURPORTIN-1 Complex
Length = 1071
Score = 26.9 bits (58), Expect = 3.5, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 80 VIKQEWKSGPRRSLLKLRKYIVG 102
VIK WK PR ++KY+VG
Sbjct: 86 VIKTRWKILPRNQCEGIKKYVVG 108
>pdb|3GJX|A Chain A, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3GJX|D Chain D, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3NBY|A Chain A, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBY|D Chain D, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBZ|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NBZ|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NC0|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC0|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC1|A Chain A, Crystal Structure Of The Crm1-Rangtp Complex
Length = 1073
Score = 26.9 bits (58), Expect = 3.5, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 80 VIKQEWKSGPRRSLLKLRKYIVG 102
VIK WK PR ++KY+VG
Sbjct: 88 VIKTRWKILPRNQCEGIKKYVVG 110
>pdb|2PSH|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSH|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 319
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 12/49 (24%)
Query: 10 IVKNNNAYLMKADNIKKWF-SKEPG-----------NLPNLASFKYSGL 46
IV+N NAYL +D++ K F +PG PN A K GL
Sbjct: 236 IVRNYNAYLRASDDLPKLFIESDPGFFSNAIVEGAKKFPNTAFVKVKGL 284
>pdb|2PSD|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSE|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 318
Score = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 10 IVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 235 IVRNYNAYLRASDDLPKLFIESDPGFFSN 263
>pdb|2PSJ|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSJ|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 319
Score = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 10 IVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 236 IVRNYNAYLRASDDLPKLFIESDPGFFSN 264
>pdb|2PSF|A Chain A, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
pdb|2PSF|B Chain B, Crystal Structures Of The Luciferase And Green Fluorescent
Protein From Renilla Reniformis
Length = 310
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 10 IVKNNNAYLMKADNIKKWF-SKEPGNLPN 37
IV+N NAYL +D++ K F +PG N
Sbjct: 235 IVRNYNAYLRASDDLPKLFIESDPGFFSN 263
>pdb|2BMO|A Chain A, The Crystal Structure Of Nitrobenzene Dioxygenase
pdb|2BMQ|A Chain A, The Crystal Structure Of Nitrobenzene Dioxygenase In
Complex With Nitrobenzene
pdb|2BMR|A Chain A, The Crystal Structure Of Nitrobenzene Dioxygenase In
Complex With 3-Nitrotoluene
Length = 447
Score = 26.2 bits (56), Expect = 7.2, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 76 PGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAALRRA 117
PGK V+K WKS + VG+ Y T AA RA
Sbjct: 184 PGKVVVKANWKS--------FAENFVGDGYHVGWTHAAALRA 217
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
0.314 0.128 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,197,141
Number of Sequences: 62578
Number of extensions: 157027
Number of successful extensions: 723
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 705
Number of HSP's gapped (non-prelim): 26
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)