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= psy10067
(124 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKQ|GG Chain g, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 204
Score = 183 bits (464), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 86/100 (86%), Positives = 93/100 (93%), Gaps = 2/100 (2%)
Query: 26 AAPA--ELPEIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQC 83
AAPA E P+IKLFG+WS DDVQ++D+SLQDYIAVKEK AK+LPHSAGRYAAKRFRKAQC
Sbjct: 7 AAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQC 66
Query: 84 PIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
PIVERLTNS+MMHGRNN KKLM VRIVKHAFEIIHLLTGE
Sbjct: 67 PIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGE 106
>pdb|3IZ6|F Chain F, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 200
Score = 146 bits (368), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 68/88 (77%), Positives = 78/88 (88%), Gaps = 1/88 (1%)
Query: 35 KLFGRWSCDDVQVSDMSLQDYIAVKE-KNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSL 93
KLF WS +DVQV+D+SL DY+AV K+A +LPH+AGRY+AKRFRKAQCP+VERLTNSL
Sbjct: 13 KLFNCWSFEDVQVNDISLADYLAVSSTKHATYLPHTAGRYSAKRFRKAQCPLVERLTNSL 72
Query: 94 MMHGRNNAKKLMAVRIVKHAFEIIHLLT 121
MMHGRNN KK+MAVRIVKHA EIIHLLT
Sbjct: 73 MMHGRNNGKKIMAVRIVKHAMEIIHLLT 100
>pdb|3IZB|F Chain F, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 225
Score = 129 bits (324), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 58/91 (63%), Positives = 74/91 (81%), Gaps = 2/91 (2%)
Query: 33 EIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNS 92
EIKLF +WS ++V+V D SL DY+ V++ F+ H+AGRYA KRFRKAQCPI+ERLTNS
Sbjct: 39 EIKLFNKWSFEEVEVKDASLVDYVQVRQ--PIFVAHTAGRYANKRFRKAQCPIIERLTNS 96
Query: 93 LMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
LMM+GRNN KKL AVRI+KH +II++LT +
Sbjct: 97 LMMNGRNNGKKLKAVRIIKHTLDIINVLTDQ 127
>pdb|3JYV|G Chain G, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 186
Score = 126 bits (317), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 57/90 (63%), Positives = 73/90 (81%), Gaps = 2/90 (2%)
Query: 34 IKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSL 93
IKLF +WS ++V+V D SL DY+ V++ F+ H+AGRYA KRFRKAQCPI+ERLTNSL
Sbjct: 1 IKLFNKWSFEEVEVKDASLVDYVQVRQ--PIFVAHTAGRYANKRFRKAQCPIIERLTNSL 58
Query: 94 MMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
MM+GRNN KKL AVRI+KH +II++LT +
Sbjct: 59 MMNGRNNGKKLKAVRIIKHTLDIINVLTDQ 88
>pdb|2XZM|G Chain G, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|G Chain G, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 200
Score = 118 bits (295), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 51/89 (57%), Positives = 68/89 (76%), Gaps = 1/89 (1%)
Query: 35 KLFGRWSCDDVQVSDMSLQDYIA-VKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSL 93
KLFG+W+ D+V++ D Q+YIA K+ F+PH+AGRY K+FRK QCPIVERL +L
Sbjct: 12 KLFGKWNYDEVKIQDPCFQNYIACTTTKSQVFVPHTAGRYQVKKFRKTQCPIVERLIGTL 71
Query: 94 MMHGRNNAKKLMAVRIVKHAFEIIHLLTG 122
M HGRN KK + +++VK+AFEIIHL+TG
Sbjct: 72 MFHGRNAGKKALCIKVVKNAFEIIHLVTG 100
>pdb|3J0L|T Chain T, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0O|T Chain T, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9a Cryo-Em Map: Classic Pre State 2
Length = 192
Score = 118 bits (295), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 51/89 (57%), Positives = 68/89 (76%), Gaps = 1/89 (1%)
Query: 35 KLFGRWSCDDVQVSDMSLQDYIA-VKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSL 93
KLFG+W+ D+V++ D Q+YIA K+ F+PH+AGRY K+FRK QCPIVERL +L
Sbjct: 4 KLFGKWNYDEVKIQDPCFQNYIACTTTKSQVFVPHTAGRYQVKKFRKTQCPIVERLIGTL 63
Query: 94 MMHGRNNAKKLMAVRIVKHAFEIIHLLTG 122
M HGRN KK + +++VK+AFEIIHL+TG
Sbjct: 64 MFHGRNAGKKALCIKVVKNAFEIIHLVTG 92
>pdb|3ZEY|2 Chain 2, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 190
Score = 112 bits (279), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 50/89 (56%), Positives = 66/89 (74%), Gaps = 3/89 (3%)
Query: 35 KLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLM 94
KLF +WS +++Q ++++L DYI + ++PHSAGR+ KRFRKA+ PIVERLTN LM
Sbjct: 7 KLFNKWSYENLQTTEIALNDYIT---RTPTYVPHSAGRWQKKRFRKARIPIVERLTNGLM 63
Query: 95 MHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
GR N KKL AVR+V+H EIIHLLT +
Sbjct: 64 FKGRGNGKKLQAVRLVRHTLEIIHLLTDQ 92
>pdb|1S1H|G Chain G, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
In File 1s1i.
pdb|2NOQ|F Chain F, Structure Of Ribosome-Bound Cricket Paralysis Virus Ires
Rna
Length = 150
Score = 90.5 bits (223), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 39/52 (75%), Positives = 46/52 (88%)
Query: 72 RYAAKRFRKAQCPIVERLTNSLMMHGRNNAKKLMAVRIVKHAFEIIHLLTGE 123
RYA KRFRKAQCPI+ERLTNSLMM+GRNN KKL AVRI+KH +II++LT +
Sbjct: 1 RYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQ 52
>pdb|3J20|H Chain H, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 215
Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 45/107 (42%), Positives = 61/107 (57%), Gaps = 19/107 (17%)
Query: 33 EIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNS 92
EIK+ GRWS +DV+V D SL+ YI ++ + LPH+ GR+A K F KA IVERL N
Sbjct: 14 EIKVMGRWSTEDVEVRDPSLKPYINLE---PRLLPHTHGRHAKKHFGKANVHIVERLINK 70
Query: 93 LMMHGRN----------------NAKKLMAVRIVKHAFEIIHLLTGE 123
+M G + N+KK+ A +VK AF+II TG+
Sbjct: 71 IMRSGGSHYKVAGHFMRREHRSLNSKKVKAYEVVKEAFKIIEQRTGK 117
>pdb|1IQV|A Chain A, Crystal Structure Analysis Of The Archaebacterial
Ribosomal Protein S7
Length = 218
Score = 77.0 bits (188), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 45/107 (42%), Positives = 61/107 (57%), Gaps = 19/107 (17%)
Query: 33 EIKLFGRWSCDDVQVSDMSLQDYIAVKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNS 92
EIK+ GRWS +DV+V D SL+ YI ++ + LPH+ GR+A K F KA IVERL N
Sbjct: 17 EIKVMGRWSTEDVEVKDPSLKPYINLE---PRLLPHTHGRHAKKHFGKANVHIVERLINK 73
Query: 93 LMMHGRN----------------NAKKLMAVRIVKHAFEIIHLLTGE 123
+M G + N+KK+ A +VK AF+II TG+
Sbjct: 74 VMRSGGSHYKVAGHFMRREHRSLNSKKVRAYEVVKEAFKIIEKRTGK 120
>pdb|3VSR|A Chain A, Arthrobacter Sp. K-1 Beta-Fructofuranosidase
pdb|3VSS|A Chain A, Arthrobacter Sp. K-1 Beta-Fructofuranosidase Complexed
With Fructose
Length = 496
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 21/100 (21%), Positives = 33/100 (33%), Gaps = 9/100 (9%)
Query: 7 ADPAYPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIA--------- 57
+DP PS P ++ P + P++ W D ++D Y
Sbjct: 40 SDPTAPSRENSMPASVTMPTVPQDFPDMSNEQVWVWDTWPLTDEDANQYSVNGWEIIFSL 99
Query: 58 VKEKNAKFLPHSAGRYAAKRFRKAQCPIVERLTNSLMMHG 97
V ++N F +R A P ER N +G
Sbjct: 100 VADRNLGFDDRHVFAKIGYFYRPAGVPAAERPENGGWTYG 139
>pdb|2C0A|A Chain A, Mechanism Of The Class I Kdpg Aldolase
pdb|2C0A|B Chain B, Mechanism Of The Class I Kdpg Aldolase
pdb|2C0A|C Chain C, Mechanism Of The Class I Kdpg Aldolase
pdb|1WBH|A Chain A, Crystal Structure Of The E45n Mutant From Kdpg Aldolase
From Escherichia Coli
pdb|1WBH|B Chain B, Crystal Structure Of The E45n Mutant From Kdpg Aldolase
From Escherichia Coli
pdb|1WBH|C Chain C, Crystal Structure Of The E45n Mutant From Kdpg Aldolase
From Escherichia Coli
Length = 214
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 11 YPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVK 59
+P+E+ GG L +IA P +++ C +S + +DY+A+K
Sbjct: 136 FPAEANGGVKALQAIAGP--FSQVRF-----CPTGGISPANYRDYLALK 177
>pdb|1WAU|A Chain A, Structure Of Kdpg Aldolase E45n Mutant
Length = 213
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 11 YPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVK 59
+P+E+ GG L +IA P +++ C +S + +DY+A+K
Sbjct: 135 FPAEANGGVKALQAIAGP--FSQVRF-----CPTGGISPANYRDYLALK 176
>pdb|1FQ0|A Chain A, Kdpg Aldolase From Escherichia Coli
pdb|1FQ0|B Chain B, Kdpg Aldolase From Escherichia Coli
pdb|1FQ0|C Chain C, Kdpg Aldolase From Escherichia Coli
pdb|1EUA|A Chain A, Schiff Base Intermediate In Kdpg Aldolase From Escherichia
Coli
pdb|1EUA|B Chain B, Schiff Base Intermediate In Kdpg Aldolase From Escherichia
Coli
pdb|1EUA|C Chain C, Schiff Base Intermediate In Kdpg Aldolase From Escherichia
Coli
pdb|1EUN|A Chain A, Structure Of 2-keto-3-deoxy-6-phosphogluconate Aldolase
From Escherichia Coli
pdb|1EUN|B Chain B, Structure Of 2-keto-3-deoxy-6-phosphogluconate Aldolase
From Escherichia Coli
pdb|1EUN|C Chain C, Structure Of 2-keto-3-deoxy-6-phosphogluconate Aldolase
From Escherichia Coli
Length = 213
Score = 25.4 bits (54), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 11 YPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVK 59
+P+E+ GG L +IA P +++ C +S + +DY+A+K
Sbjct: 135 FPAEANGGVKALQAIAGP--FSQVRF-----CPTGGISPANYRDYLALK 176
>pdb|1FWR|A Chain A, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
pdb|1FWR|B Chain B, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
pdb|1FWR|C Chain C, Crystal Structure Of Kdpg Aldolase Double Mutant
K133qT161K
Length = 213
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 11 YPSESTGGPVGLSSIAAPAELPEIKLFGRWSCDDVQVSDMSLQDYIAVK 59
+P+E+ GG L +IA P +++ C +S + +DY+A+K
Sbjct: 135 FPAEANGGVKALQAIAGP--FSQVRF-----CPKGGISPANYRDYLALK 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
0.319 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,635,626
Number of Sequences: 62578
Number of extensions: 124988
Number of successful extensions: 216
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 15
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
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: 45 (21.9 bits)