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= psy6286
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 111 bits (278), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 60/173 (34%), Positives = 93/173 (53%), Gaps = 41/173 (23%)
Query: 20 GYATEADVIEMKGRVACELSKSEETVI--LTINDKL------------------------ 53
G+ T D+IE+KGRVACE+S +E ++ L N
Sbjct: 830 GFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEA 889
Query: 54 ---------------ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLK 98
E+A IA+I +SK+++ E YV F+ LM+VV+ WC GA+F +
Sbjct: 890 PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQ 949
Query: 99 VCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
+C +TD++EGS+IR +RLEE++++LV + IGN+ L+EK +K + RDI
Sbjct: 950 ICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDI 1002
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 111 bits (277), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 60/173 (34%), Positives = 93/173 (53%), Gaps = 41/173 (23%)
Query: 20 GYATEADVIEMKGRVACELSKSEETVI--LTINDKL------------------------ 53
G+ T D+IE+KGRVACE+S +E ++ L N
Sbjct: 928 GFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQERCKEA 987
Query: 54 ---------------ELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWCEGASFLK 98
E+A IA+I +SK+++ E YV F+ LM+VV+ WC GA+F +
Sbjct: 988 PRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRGATFTQ 1047
Query: 99 VCSITDIFEGSIIRCMRRLEEVLRQLVQASRNIGNTLLEEKFNEAIKTVKRDI 151
+C +TD++EGS+IR +RLEE++++LV + IGN+ L+EK +K + RDI
Sbjct: 1048 ICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDI 1100
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 53/85 (62%)
Query: 67 KLDLDEDSYVNQFKPSLMDVVHAWCEGASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQ 126
L DE ++++ + ++M+VV+ W G SF ++ ++ EG+++R + L+E+ R++
Sbjct: 905 PLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKT 964
Query: 127 ASRNIGNTLLEEKFNEAIKTVKRDI 151
AS IGN+ L K + A + +KRDI
Sbjct: 965 ASIIIGNSTLHMKMSRAQELIKRDI 989
>pdb|1WB7|A Chain A, Iron Superoxide Dismutase (Fe-Sod) From The
Hyperthermophile Sulfolobus Solfataricus. Crystal
Structure Of The Y41f Mutant.
pdb|1WB7|B Chain B, Iron Superoxide Dismutase (Fe-Sod) From The
Hyperthermophile Sulfolobus Solfataricus. Crystal
Structure Of The Y41f Mutant
Length = 210
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 39 SKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWC 91
++S I+T + + HIA I I LD E +Y Q+K D V+AW
Sbjct: 142 TESGNLQIMTFENHFQ--NHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWW 192
>pdb|1WB8|A Chain A, Iron Superoxide Dismutase (Fe-Sod) From The
Hyperthermophile Sulfolobus Solfataricus. 2.3 A
Resolution Structure Of Recombinant Protein With A
Covalently Modified Tyrosin In The Active Site.
pdb|1WB8|B Chain B, Iron Superoxide Dismutase (Fe-Sod) From The
Hyperthermophile Sulfolobus Solfataricus. 2.3 A
Resolution Structure Of Recombinant Protein With A
Covalently Modified Tyrosin In The Active Site
Length = 210
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 39 SKSEETVILTINDKLELARHIARISIESKLDLDEDSYVNQFKPSLMDVVHAWC 91
++S I+T + + HIA I I LD E +Y Q+K D V+AW
Sbjct: 142 TESGNLQIMTFENHFQ--NHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWW 192
>pdb|1MUK|A Chain A, Reovirus Lambda3 Native Structure
pdb|1MWH|A Chain A, Reovirus Polymerase Lambda3 Bound To Mrna Cap Analog
pdb|1N1H|A Chain A, Initiation Complex Of Polymerase Lambda3 From Reovirus
pdb|1N35|A Chain A, Lambda3 Elongation Complex With Four Phosphodiester Bond
Formed
pdb|1N38|A Chain A, Reovirus Polymerase Lambda3 Elongation Complex With One
Phosphodiester Bond Formed
pdb|1UON|A Chain A, Reovirus Polymerase Lambda-3 Localized By Electron
Cryomicroscopy Of Virions At 7.6-a Resolution
Length = 1267
Score = 26.6 bits (57), Expect = 6.1, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 81 PSLMDVVHAWCEGASFLKVCSITDIFE--GSIIRCMRRLEEVLRQLVQA 127
PSL DV H W +GA + + ++ E +++R R +L++A
Sbjct: 1007 PSLFDVPHKWYQGAQEAAIATREELAEMDETLMRARRHSYSSFSKLLEA 1055
>pdb|3KSF|A Chain A, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|B Chain B, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|C Chain C, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|D Chain D, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|E Chain E, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|F Chain F, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|G Chain G, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSF|H Chain H, Structure Of Frmsr Of Staphylococcus Aureus (Reduced Form)
pdb|3KSH|A Chain A, Structure Of Frmsr Of Staphylococcus Aureus (Oxidized
Form)
pdb|3KSI|A Chain A, Structure Of Frmsr Of Staphylococcus Aureus (Complex With
2-
Length = 160
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 25 ADVIEMKGRVACEL-SKSEETVILTINDKL 53
ADV + KG +AC+ SKSE V + +DK+
Sbjct: 97 ADVHQFKGHIACDANSKSEIVVPIFKDDKI 126
>pdb|3KSG|A Chain A, Structure Of Frmsr Of Staphylococcus Aureus (Complex With
Su
pdb|3KSG|B Chain B, Structure Of Frmsr Of Staphylococcus Aureus (Complex With
Su
Length = 160
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 25 ADVIEMKGRVACEL-SKSEETVILTINDKL 53
ADV + KG +AC+ SKSE V + +DK+
Sbjct: 97 ADVHQFKGHIACDANSKSEIVVPIFKDDKI 126
>pdb|1VB5|A Chain A, Crystal Structure Analysis Of The Pyrococcus Horikoshii
Ot3 Translation Initiation Factor Eif-2b
pdb|1VB5|B Chain B, Crystal Structure Analysis Of The Pyrococcus Horikoshii
Ot3 Translation Initiation Factor Eif-2b
Length = 276
Score = 26.2 bits (56), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 94 ASFLKVCSITDIFEGSIIRCMRRLEEVLRQLVQASRNI---GNTLLEEKFN----EAIKT 146
A F+ V + DI + + +RR+EE R+L + G+ ++ F+ E I+T
Sbjct: 69 ARFIPVTNRRDILKSRALEFLRRMEEAKRELASIGAQLIDDGDVIITHSFSSTVLEIIRT 128
Query: 147 VK 148
K
Sbjct: 129 AK 130
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
0.322 0.136 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,025,219
Number of Sequences: 62578
Number of extensions: 142284
Number of successful extensions: 465
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 457
Number of HSP's gapped (non-prelim): 13
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)