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= 033029
(129 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 = 214 bits (544), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 104/141 (73%), Positives = 117/141 (82%), Gaps = 14/141 (9%)
Query: 2 ATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASM 47
+TARTVKDV+PHEFVKAYSAHLKRSGK FKEL PYDPDWYY RAAS+
Sbjct: 4 STARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASI 63
Query: 48 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107
ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++PKGG
Sbjct: 64 ARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGG 123
Query: 108 RRITSSGQRDLDQVAGRIVVA 128
R ITS G+RDLDQVAGR+ V
Sbjct: 124 RLITSQGRRDLDQVAGRVDVT 144
>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 = 119 bits (297), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 57/136 (41%), Positives = 89/136 (65%), Gaps = 15/136 (11%)
Query: 6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPD-WYYVRAASMARK 50
+V+DV+ +F+ AY++ L+R GK + E+ P D + W+Y RAAS+AR
Sbjct: 2 SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 61
Query: 51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110
IY+R+ +GVG ++YGG+K G RP +SG+I R +LQ L+ + I++I PKGGRRI
Sbjct: 62 IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 121
Query: 111 TSSGQRDLDQVAGRIV 126
+ +GQRDLD++A + +
Sbjct: 122 SENGQRDLDRIAAQTL 137
>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 = 118 bits (296), Expect = 9e-28, Method: Compositional matrix adjust.
Identities = 57/136 (41%), Positives = 89/136 (65%), Gaps = 15/136 (11%)
Query: 6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPD-WYYVRAASMARK 50
+V+DV+ +F+ AY++ L+R GK + E+ P D + W+Y RAAS+AR
Sbjct: 5 SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64
Query: 51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110
IY+R+ +GVG ++YGG+K G RP +SG+I R +LQ L+ + I++I PKGGRRI
Sbjct: 65 IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124
Query: 111 TSSGQRDLDQVAGRIV 126
+ +GQRDLD++A + +
Sbjct: 125 SENGQRDLDRIAAQTL 140
>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 = 88.2 bits (217), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 46/141 (32%), Positives = 76/141 (53%), Gaps = 19/141 (13%)
Query: 6 TVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAASMARKI 51
TVKDV+ +F++ Y++HLK++ K +ELAP D DW Y+R A++ARK+
Sbjct: 9 TVKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKV 68
Query: 52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII-----DIEPKG 106
YL+ G+ + + I+G +K G+ G I R L+ L+++ II K
Sbjct: 69 YLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKF 128
Query: 107 GRRITSSGQRDLDQVAGRIVV 127
R IT G +L+++A +I +
Sbjct: 129 SRVITKEGMTELNRIATQIAI 149
>pdb|3ZEY|O Chain O, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 167
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 42/136 (30%), Positives = 69/136 (50%), Gaps = 14/136 (10%)
Query: 6 TVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAASMARKI 51
T++DV P +VK S H K+ GK +E AP +PDWYY+R A++ R +
Sbjct: 22 TLRDVHPWRWVKICSQHFKQEGKMMVPNCAEIVKTSHGRERAPQNPDWYYIRCAAVLRAV 81
Query: 52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
YLR G+G G + + K GSRP ++S + + L + +++ G R+T
Sbjct: 82 YLRPGVGYGGLSKRFSSKKNRGSRPEITTRASKGLLHWCCKSLTKLELLEKCKGAGHRVT 141
Query: 112 SSGQRDLDQVAGRIVV 127
G++ D +A +I +
Sbjct: 142 KLGRKVADTIAFKIAL 157
>pdb|2V7F|A Chain A, Structure Of P. Abyssi Rps19 Protein
Length = 150
Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/121 (34%), Positives = 65/121 (53%), Gaps = 5/121 (4%)
Query: 5 RTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRR 64
+ + ++ P E+ A ++G+ KE P DW+Y R AS+ R++YL +G+ R
Sbjct: 21 KEIPEIKPPEW-----APFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRT 75
Query: 65 IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR 124
YGG K G P F K+ G+I R LQQL+ ++ P GR IT G+ LD++A
Sbjct: 76 YYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATE 135
Query: 125 I 125
+
Sbjct: 136 L 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 = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 42/121 (34%), Positives = 65/121 (53%), Gaps = 5/121 (4%)
Query: 5 RTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRR 64
+ + ++ P E+ A ++G+ KE P DW+Y R AS+ R++YL +G+ R
Sbjct: 21 KEIPEIKPPEW-----APFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRT 75
Query: 65 IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR 124
YGG K G P F K+ G+I R LQQL+ ++ P GR IT G+ LD++A
Sbjct: 76 YYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATE 135
Query: 125 I 125
+
Sbjct: 136 L 136
>pdb|2GAH|A Chain A, Heterotetrameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 21/50 (42%)
Query: 10 VSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGV 59
+ P +S HL +F+++ + WYY +A + R+ V
Sbjct: 571 LDPARITAXHSWHLSHGAEFEDVGQWKRPWYYPQAGETXDQAVYRESKAV 620
>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 = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 30 KELAPYDPDWYYVRAASMARKIYLRQGLGVGSFR 63
K APY ++ R+A+MA L G+G SFR
Sbjct: 6 KSAAPYHDEFPLFRSANMASPDKLSTGIGFHSFR 39
>pdb|2GAG|A Chain A, Heteroteterameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 10 VSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAA-SMARKIY 52
+ P +S HL +F+++ + WYY +A +M + +Y
Sbjct: 571 LDPARITAMHSWHLSHGAEFEDVGQWKRPWYYPQAGETMDQAVY 614
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 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,946,864
Number of Sequences: 62578
Number of extensions: 154614
Number of successful extensions: 294
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 279
Number of HSP's gapped (non-prelim): 10
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
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: 45 (21.9 bits)