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= 032244
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|S Chain S, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 146
Score = 219 bits (557), Expect = 5e-58, Method: Compositional matrix adjust.
Identities = 102/140 (72%), Positives = 119/140 (85%)
Query: 3 TAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMA 62
TA+ VKDV+PHEFVKAY+AHLKRSGK+ELP W DIVKT KEL PYDPDWYY RAAS+A
Sbjct: 5 TARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIA 64
Query: 63 RKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122
RKIYLR G+GVG F++IYGG +RNGSRPPHF KSSG+++R+IL QLQ II++D KGGR
Sbjct: 65 RKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGR 124
Query: 123 RITSSGQRDLDQVAGRIAVV 142
ITS G+RDLDQVAGR+ V
Sbjct: 125 LITSQGRRDLDQVAGRVDVT 144
>pdb|3IZB|S Chain S, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|M Chain M, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|M Chain M, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 144
Score = 134 bits (337), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 63/134 (47%), Positives = 93/134 (69%), Gaps = 1/134 (0%)
Query: 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARK 64
+V+DV+ +F+ AYA+ L+R GK+E+P + DIVKT + E+ P D + W+Y RAAS+AR
Sbjct: 5 SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64
Query: 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
IY+R +GVG ++YGG K G RP +SGS+ R +L L+ I+E+ KGGRRI
Sbjct: 65 IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124
Query: 125 TSSGQRDLDQVAGR 138
+ +GQRDLD++A +
Sbjct: 125 SENGQRDLDRIAAQ 138
>pdb|3JYV|T Chain T, 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 = 141
Score = 134 bits (337), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 63/134 (47%), Positives = 93/134 (69%), Gaps = 1/134 (0%)
Query: 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARK 64
+V+DV+ +F+ AYA+ L+R GK+E+P + DIVKT + E+ P D + W+Y RAAS+AR
Sbjct: 2 SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 61
Query: 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
IY+R +GVG ++YGG K G RP +SGS+ R +L L+ I+E+ KGGRRI
Sbjct: 62 IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 121
Query: 125 TSSGQRDLDQVAGR 138
+ +GQRDLD++A +
Sbjct: 122 SENGQRDLDRIAAQ 135
>pdb|2XZM|T Chain T, 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|T Chain T, 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 = 155
Score = 105 bits (261), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 51/140 (36%), Positives = 79/140 (56%), Gaps = 5/140 (3%)
Query: 7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
VKDV+ +F++ YA+HLK++ K+ +P + T +ELAP D DW YIR A++ARK+Y
Sbjct: 10 VKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVY 69
Query: 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-----SKGG 121
L+ G+ + + I+G K G+ G + R L L+D II D K
Sbjct: 70 LKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFS 129
Query: 122 RRITSSGQRDLDQVAGRIAV 141
R IT G +L+++A +IA+
Sbjct: 130 RVITKEGMTELNRIATQIAI 149
>pdb|3ZEY|O Chain O, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 167
Score = 98.2 bits (243), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 48/136 (35%), Positives = 76/136 (55%)
Query: 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
++DV P +VK + H K+ GK+ +P +IVKT +E AP +PDWYYIR A++ R +
Sbjct: 22 TLRDVHPWRWVKICSQHFKQEGKMMVPNCAEIVKTSHGRERAPQNPDWYYIRCAAVLRAV 81
Query: 66 YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
YLR G+G G + + K GSRP +++S + L ++E G R+T
Sbjct: 82 YLRPGVGYGGLSKRFSSKKNRGSRPEITTRASKGLLHWCCKSLTKLELLEKCKGAGHRVT 141
Query: 126 SSGQRDLDQVAGRIAV 141
G++ D +A +IA+
Sbjct: 142 KLGRKVADTIAFKIAL 157
>pdb|2V7F|A Chain A, Structure Of P. Abyssi Rps19 Protein
Length = 150
Score = 93.2 bits (230), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 52/134 (38%), Positives = 69/134 (51%)
Query: 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
V DV V+ A LK +I+ P W VKTG KE P DW+Y R AS+ R++
Sbjct: 3 TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62
Query: 66 YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
YL G +G+ R YGG K G P F K+ GS+ R L QL+ +E GR IT
Sbjct: 63 YLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122
Query: 126 SSGQRDLDQVAGRI 139
G+ LD++A +
Sbjct: 123 PKGRSFLDKIATEL 136
>pdb|3J20|U Chain U, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 150
Score = 93.2 bits (230), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 52/134 (38%), Positives = 69/134 (51%)
Query: 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
V DV V+ A LK +I+ P W VKTG KE P DW+Y R AS+ R++
Sbjct: 3 TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62
Query: 66 YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
YL G +G+ R YGG K G P F K+ GS+ R L QL+ +E GR IT
Sbjct: 63 YLDGPVGIERLRTYYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122
Query: 126 SSGQRDLDQVAGRI 139
G+ LD++A +
Sbjct: 123 PKGRSFLDKIATEL 136
>pdb|3G50|A Chain A, Crystal Structure Of Nisod D3a Mutant At 1.9 A
pdb|3G50|B Chain B, Crystal Structure Of Nisod D3a Mutant At 1.9 A
pdb|3G50|C Chain C, Crystal Structure Of Nisod D3a Mutant At 1.9 A
Length = 117
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136
+PPHF K LHQL + + L + G + ++GQ+ LD +A
Sbjct: 64 KPPHFEKYPE------LHQLVNDTLKALSAAKGSKDPATGQKALDYIA 105
>pdb|3G4X|A Chain A, Crystal Structure Of Nisod Y9f Mutant
pdb|3G4X|B Chain B, Crystal Structure Of Nisod Y9f Mutant
pdb|3G4X|C Chain C, Crystal Structure Of Nisod Y9f Mutant
pdb|3G4Z|A Chain A, Crystal Structure Of Nisod Y9f Mutant At 1.9 A
pdb|3G4Z|B Chain B, Crystal Structure Of Nisod Y9f Mutant At 1.9 A
pdb|3G4Z|C Chain C, Crystal Structure Of Nisod Y9f Mutant At 1.9 A
Length = 117
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136
+PPHF K LHQL + + L + G + ++GQ+ LD +A
Sbjct: 64 KPPHFEKYPE------LHQLVNDTLKALSAAKGSKDPATGQKALDYIA 105
>pdb|1T6Q|A Chain A, Nickel Superoxide Dismutase (nisod) Cn-treated Apo
Structure
pdb|1T6Q|B Chain B, Nickel Superoxide Dismutase (nisod) Cn-treated Apo
Structure
pdb|1T6Q|C Chain C, Nickel Superoxide Dismutase (nisod) Cn-treated Apo
Structure
pdb|1T6U|A Chain A, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|B Chain B, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|C Chain C, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|D Chain D, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|E Chain E, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|F Chain F, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|G Chain G, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|H Chain H, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|I Chain I, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|J Chain J, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|K Chain K, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
pdb|1T6U|L Chain L, Nickel Superoxide Dismutase (Nisod) Native 1.30 A
Structure
Length = 117
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136
+PPHF K LHQL + + + + G + ++GQ+ LD +A
Sbjct: 64 KPPHFEKYPE------LHQLVNDTLKAMSAAKGSKDPATGQKALDYIA 105
>pdb|3KB1|A Chain A, Crystal Structure Of The Nucleotide-Binding Protein Af_226
In Complex With Adp From Archaeoglobus Fulgidus,
Northeast Structural Genomics Consortium Target Gr157
pdb|3KB1|B Chain B, Crystal Structure Of The Nucleotide-Binding Protein Af_226
In Complex With Adp From Archaeoglobus Fulgidus,
Northeast Structural Genomics Consortium Target Gr157
Length = 262
Score = 29.3 bits (64), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 15 FVKAYAAHLKRSGKIE----LPTWNDIVKTGTLKELAPYDPDWY 54
F + A+ L R KIE +P +D++K L + Y+PDW+
Sbjct: 206 FGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWF 249
>pdb|1T6I|A Chain A, Nickel Superoxide Dismutase (nisod) Apo Structure
pdb|1T6I|B Chain B, Nickel Superoxide Dismutase (nisod) Apo Structure
pdb|1T6I|C Chain C, Nickel Superoxide Dismutase (nisod) Apo Structure
Length = 118
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136
+PPHF K LHQL + + + G + ++GQ+ LD +A
Sbjct: 65 KPPHFEKYPE------LHQLVNDTLKAXSAAKGSKDPATGQKALDYIA 106
>pdb|3FN9|A Chain A, Crystal Structure Of Putative Beta-galactosidase From
Bacteroides Fragilis
pdb|3FN9|B Chain B, Crystal Structure Of Putative Beta-galactosidase From
Bacteroides Fragilis
pdb|3FN9|C Chain C, Crystal Structure Of Putative Beta-galactosidase From
Bacteroides Fragilis
pdb|3FN9|D Chain D, Crystal Structure Of Putative Beta-galactosidase From
Bacteroides Fragilis
Length = 692
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 5/96 (5%)
Query: 29 IELP-TWNDI---VKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK 84
+E+P TWN + V++G+ E A Y + ++++LR GVG+ +Y GK
Sbjct: 39 VEIPHTWNAMDMQVQSGSFYEGAGYYRKTQFFPHDLEGKRVFLRFE-GVGACAEVYVNGK 97
Query: 85 RNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
G+ +S + + + ++ I++ D+K
Sbjct: 98 LAGTHKGGYSAFACEIGTALKLGAENEIIVKADNKA 133
>pdb|2XZI|A Chain A, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
pdb|2XZI|B Chain B, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
pdb|2XZJ|A Chain A, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
pdb|2XZJ|B Chain B, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
pdb|2XZK|A Chain A, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
pdb|2XZK|B Chain B, The Aspergillus Fumigatus Sialidase Is A Kdnase:
Structural And Mechanistic Insights
Length = 386
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 44 KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFR 77
K APY ++ R+A+MA L G+G SFR
Sbjct: 6 KSAAPYHDEFPLFRSANMASPDKLSTGIGFHSFR 39
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
0.317 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,583,226
Number of Sequences: 62578
Number of extensions: 194161
Number of successful extensions: 434
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 423
Number of HSP's gapped (non-prelim): 18
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)