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= psy6711
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T9K|A Chain A, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
Translation Initiation Factor [thermotoga Maritima]
pdb|1T9K|B Chain B, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
Translation Initiation Factor [thermotoga Maritima]
pdb|1T9K|C Chain C, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
Translation Initiation Factor [thermotoga Maritima]
pdb|1T9K|D Chain D, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
Translation Initiation Factor [thermotoga Maritima]
Length = 347
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 35/50 (70%)
Query: 12 IAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVA 61
+AV AK + +PF++AAP ++ID I +G+ I IEER +E+TH G +A
Sbjct: 253 LAVLAKRNNIPFYVAAPVSTIDPTIRSGEEIPIEERRPEEVTHCGGNRIA 302
>pdb|1T5O|A Chain A, Crystal Structure Of The Translation Initiation Factor
Eif-2b, Subunit Delta, From A. Fulgidus
pdb|1T5O|B Chain B, Crystal Structure Of The Translation Initiation Factor
Eif-2b, Subunit Delta, From A. Fulgidus
pdb|1T5O|C Chain C, Crystal Structure Of The Translation Initiation Factor
Eif-2b, Subunit Delta, From A. Fulgidus
pdb|1T5O|D Chain D, Crystal Structure Of The Translation Initiation Factor
Eif-2b, Subunit Delta, From A. Fulgidus
Length = 351
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 12 IAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVA 61
++V AKHH +PF++AAP + D + D +VIEERP +E+ +A
Sbjct: 250 VSVVAKHHNIPFYVAAPKATFDWERTAKD-VVIEERPREELIFCGKRQIA 298
>pdb|2YRF|A Chain A, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase From Bacillus Subtilis Complexed With Sulfate
Ion
pdb|2YRF|B Chain B, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase From Bacillus Subtilis Complexed With Sulfate
Ion
pdb|2YVK|A Chain A, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase Product Complex From Bacillus Subtilis
pdb|2YVK|B Chain B, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase Product Complex From Bacillus Subtilis
pdb|2YVK|C Chain C, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase Product Complex From Bacillus Subtilis
pdb|2YVK|D Chain D, Crystal Structure Of 5-Methylthioribose 1-Phosphate
Isomerase Product Complex From Bacillus Subtilis
Length = 374
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 32/53 (60%)
Query: 12 IAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAGIHVAASD 64
+A+ A +PFF+AAP ++ D + G I IEER +E+ ++G+ A S+
Sbjct: 278 LAILANAFDIPFFVAAPLSTFDTKVKCGADIPIEERDPEEVRQISGVRTAPSN 330
>pdb|2A0U|A Chain A, Crystal Structure Of The Eukaryotic Initiation Factor 2b
From Leishmania Major At 2.1 A Resolution
pdb|2A0U|B Chain B, Crystal Structure Of The Eukaryotic Initiation Factor 2b
From Leishmania Major At 2.1 A Resolution
Length = 383
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 29/42 (69%)
Query: 12 IAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMT 53
+AVSAK H V ++AAP T++D+ +G+ + IEER E+T
Sbjct: 282 LAVSAKFHGVKLYVAAPTTTLDVKTASGNHVEIEEREPTEIT 323
>pdb|1W2W|B Chain B, Crystal Structure Of Yeast Ypr118w, A Methylthioribose-1-
Phosphate Isomerase Related To Regulatory Eif2b Subunits
pdb|1W2W|F Chain F, Crystal Structure Of Yeast Ypr118w, A Methylthioribose-1-
Phosphate Isomerase Related To Regulatory Eif2b Subunits
pdb|1W2W|J Chain J, Crystal Structure Of Yeast Ypr118w, A Methylthioribose-1-
Phosphate Isomerase Related To Regulatory Eif2b Subunits
pdb|1W2W|N Chain N, Crystal Structure Of Yeast Ypr118w, A Methylthioribose-1-
Phosphate Isomerase Related To Regulatory Eif2b Subunits
Length = 191
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 28/48 (58%)
Query: 10 LQIAVSAKHHKVPFFIAAPWTSIDLDIPNGDAIVIEERPSQEMTHVAG 57
LQ+AV K + FF+ AP T+ID GD I++EER +E V G
Sbjct: 75 LQLAVICKQFGIKFFVVAPKTTIDNVTETGDDIIVEERNPEEFKVVTG 122
>pdb|2DDR|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Calcium Ion
pdb|2DDR|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Calcium Ion
pdb|2DDR|C Chain C, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Calcium Ion
pdb|2DDR|D Chain D, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Calcium Ion
pdb|2DDS|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Cobalt Ion
pdb|2DDS|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Cobalt Ion
pdb|2DDS|C Chain C, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Cobalt Ion
pdb|2DDS|D Chain D, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Cobalt Ion
pdb|2DDT|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Magnesium Ion
pdb|2DDT|B Chain B, Crystal Structure Of Sphingomyelinase From Bacillus Cereus
With Magnesium Ion
Length = 306
Score = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 35 DIPNGDAIVIEERPSQEMTHVAGIHVAASD--CGSKGTFQSHSGSINKVEDLPEMSIVEL 92
++ N + + + + HV G H+ A D CG + + +++D + +
Sbjct: 127 NLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPN 186
Query: 93 EDVKIIQDDHTIHKMSARIN 112
+ +I D ++K++A N
Sbjct: 187 NEYVLIGGDMNVNKINAENN 206
>pdb|2UYR|X Chain X, Crystal Structure Of Bacillus Cereus Sphingomyelinase
Mutant :n57a
Length = 306
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 35 DIPNGDAIVIEERPSQEMTHVAGIHVAASD--CGSKGTFQSHSGSINKVEDLPEMSIVEL 92
++ N + + + + HV G H+ A D CG + + +++D + +
Sbjct: 127 NLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPN 186
Query: 93 EDVKIIQDDHTIHKMSARIN 112
+ +I D ++K++A N
Sbjct: 187 NEYVLIGGDMNVNKINAENN 206
>pdb|3B0H|A Chain A, Assimilatory Nitrite Reductase (Nii4) From Tobbaco Root
pdb|3B0H|B Chain B, Assimilatory Nitrite Reductase (Nii4) From Tobbaco Root
Length = 588
Score = 26.2 bits (56), Expect = 5.5, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 79 NKVEDLPEMSIVELEDVKIIQDD 101
N +EDL ++S+ E+E K+ +DD
Sbjct: 89 NGIEDLAKISLEEIEGSKLTKDD 111
>pdb|2BHR|A Chain A, Dengue Virus Rna Helicase
pdb|2BHR|B Chain B, Dengue Virus Rna Helicase
pdb|2BMF|A Chain A, Dengue Virus Rna Helicase At 2.4a
pdb|2BMF|B Chain B, Dengue Virus Rna Helicase At 2.4a
Length = 451
Score = 25.8 bits (55), Expect = 8.0, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 51 EMTHVAGIHVAASDCGSKGTF-QSHSGSINKVEDLPEMS 88
EM AGI + A+ GS+ F QS++ +++ ++PE S
Sbjct: 138 EMGEAAGIFMTATPPGSRDPFPQSNAPIMDEEREIPERS 176
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 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,130,962
Number of Sequences: 62578
Number of extensions: 151692
Number of successful extensions: 307
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 300
Number of HSP's gapped (non-prelim): 11
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)