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= 032727
(135 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|U Chain U, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 138
Score = 220 bits (560), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 109/126 (86%), Positives = 119/126 (94%), Gaps = 3/126 (2%)
Query: 1 MADTK---AVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNA 57
MADTK AVTLRTRKFMTNRLLSRKQFV++VLHPGRANVSKA+LKEKLA++YEVKD N
Sbjct: 1 MADTKTAPAVTLRTRKFMTNRLLSRKQFVLEVLHPGRANVSKADLKEKLAKLYEVKDSNC 60
Query: 58 IFVFKFRTHFGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVEKSRKQLKERKNRA 117
IFVFKFRTHFGGGKSTGFGLIYD+++ AKK+EPKYRLIRNGL TKVEKSRKQ+KERKNRA
Sbjct: 61 IFVFKFRTHFGGGKSTGFGLIYDNLDAAKKYEPKYRLIRNGLATKVEKSRKQMKERKNRA 120
Query: 118 KKIRGV 123
KKIRGV
Sbjct: 121 KKIRGV 126
>pdb|3IZB|U Chain U, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5C|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|D Chain D, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 135
Score = 153 bits (387), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 81/123 (65%), Positives = 99/123 (80%), Gaps = 4/123 (3%)
Query: 1 MADTKAVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFV 60
M+D AVT+RTRK ++N LL+RKQFV+DVLHP RANVSK EL+EKLA +Y+ + +A+ V
Sbjct: 1 MSD--AVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKA-EKDAVSV 57
Query: 61 FKFRTHFGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVEK-SRKQLKERKNRAKK 119
F FRT FGGGKS GFGL+Y+SV AKKFEP YRL+R GL KVEK SR+Q K++KNR KK
Sbjct: 58 FGFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKK 117
Query: 120 IRG 122
I G
Sbjct: 118 IFG 120
>pdb|2XZM|P Chain P, 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|P Chain P, 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 = 149
Score = 94.7 bits (234), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 47/117 (40%), Positives = 73/117 (62%), Gaps = 1/117 (0%)
Query: 6 AVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRT 65
+ +RT+K + N LLSR+Q +DVLHP SK +++E+LA+ +V D + V+ F T
Sbjct: 2 TIVIRTKKILVNPLLSRRQLSLDVLHPDSPTASKEKIREELAKQLKV-DARNVVVYGFST 60
Query: 66 HFGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVEKSRKQLKERKNRAKKIRG 122
+GGGKSTGF L+YD+ + K+EP YRL + + + +R+ KE K + K+ G
Sbjct: 61 QYGGGKSTGFALVYDNQQYLLKYEPNYRLRKVKILGEKPNTRRSFKELKRKIKRTSG 117
>pdb|3ZEY|T Chain T, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 137
Score = 88.6 bits (218), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 63/117 (53%), Positives = 82/117 (70%), Gaps = 1/117 (0%)
Query: 7 VTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAEL-KEKLARMYEVKDPNAIFVFKFRT 65
VT+RT +F N+LL+RKQFV++V HPG A+L + +LA +Y+V D N I VF F+T
Sbjct: 10 VTVRTSQFKVNKLLNRKQFVVEVNHPGWCGTVPAKLIRNRLASLYKVADENQISVFGFKT 69
Query: 66 HFGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVEKSRKQLKERKNRAKKIRG 122
FGGGK+TGFGLIYD + K+ EP YR R G+ K +RK +KER+NR KKIRG
Sbjct: 70 KFGGGKTTGFGLIYDDLAAMKRIEPNYRKARLGMGKKKLPARKSVKERRNRNKKIRG 126
>pdb|3J20|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|6 Chain 6, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 99
Score = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 54/98 (55%), Gaps = 1/98 (1%)
Query: 7 VTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTH 66
+ +R ++ N+L+ RK+ ++ HPG S+ ++K KL M ++ +P + R++
Sbjct: 1 MEIRIKEIKENKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAMLDL-NPETTVIQYIRSY 59
Query: 67 FGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVE 104
FG S G+ YDS E EP+Y LIR+GL K E
Sbjct: 60 FGSYISKGYAKAYDSKERMLYIEPEYILIRDGLIEKKE 97
>pdb|2V94|A Chain A, Crystal Structure Of P. Abyssi Rps24
pdb|2V94|B Chain B, Crystal Structure Of P. Abyssi Rps24
Length = 107
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 17 NRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFG 76
N+L+ RK+ ++ HPG S+ ++K KL ++ +P + R++FG KS G+
Sbjct: 19 NKLIGRKEIYFEIYHPGEPTPSRKDVKGKLVAXLDL-NPETTVIQYIRSYFGSYKSKGYA 77
Query: 77 LIYDSVENAKKFEPKYRLIRNGLDTKVE 104
Y + EP+Y LIR+G+ K E
Sbjct: 78 KYYYDKDRXLYIEPEYILIRDGIIEKKE 105
>pdb|2G1D|A Chain A, Solution Structure Of Ribosomal Protein S24e From
Thermoplasma Acidophilum
Length = 98
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 17 NRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFG 76
N +L RK+ + S+ E+KE +A+ +E D + V + G + G+
Sbjct: 11 NPILKRKEIKYVLKFDSSRTPSREEIKELIAK-HEGVDKELVIVDNNKQLTGKHEIEGYT 69
Query: 77 LIYDSVENAKKFEPKYRLIRNGLDTK 102
IY +A +EP Y LIRNGL K
Sbjct: 70 KIYADKPSAMLYEPDYELIRNGLKQK 95
>pdb|1XN9|A Chain A, Solution Structure Of Methanosarcina Mazei Protein
Rps24e: The Northeast Structural Genomics Consortium
Target Mar11
Length = 101
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 46/84 (54%), Gaps = 4/84 (4%)
Query: 17 NRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK-FRTHFGGGKSTGF 75
N LL+R++ V + G + S+ +++ KLA M + P + V + +T +G +S G+
Sbjct: 11 NPLLNRRELDFIVKYEG-STPSRNDVRNKLAAM--LNAPLELLVIQRIKTEYGMQESKGY 67
Query: 76 GLIYDSVENAKKFEPKYRLIRNGL 99
+Y+ + K+ E +Y L RN +
Sbjct: 68 AKLYEDADRMKQVEQEYVLKRNAV 91
>pdb|2Q32|A Chain A, Crystal Structure Of Human Heme Oxygenase-2 C127a (Ho-2)
pdb|2Q32|B Chain B, Crystal Structure Of Human Heme Oxygenase-2 C127a (Ho-2)
pdb|2QPP|A Chain A, Crystal Structure Of Human Heme Oxygenase-2 C127a (Ho-2)
With Bound Heme
pdb|2QPP|B Chain B, Crystal Structure Of Human Heme Oxygenase-2 C127a (Ho-2)
With Bound Heme
pdb|2RGZ|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
Human Heme Oxygenase-2 C127a (Ho-2) With Bound Heme
pdb|2RGZ|B Chain B, Ensemble Refinement Of The Protein Crystal Structure Of
Human Heme Oxygenase-2 C127a (Ho-2) With Bound Heme
Length = 264
Score = 29.3 bits (64), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 32/49 (65%), Gaps = 4/49 (8%)
Query: 72 STGFG---LIYDSVENAKKFEPKYRLIRNGLDTKVEKSRKQLKERKNRA 117
STG G ++++V+NA++F+ YR N LD + K+++++ E N+A
Sbjct: 179 STGEGTQFYLFENVDNAQQFKQLYRARMNALDLNM-KTKERIVEEANKA 226
>pdb|4BAA|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
pdb|4BAA|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A Beta-
Phenylalanine Ammonia Lyase
Length = 705
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 87 KFEPKYRLIRNGLDTKVEKSRKQLKERKNRAK 118
KF P YR +R LDT V +R++ +++ K
Sbjct: 642 KFLPFYRFVREELDTGVMSARREQTPQEDVQK 673
>pdb|2YII|A Chain A, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|B Chain B, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|C Chain C, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|2YII|D Chain D, Manipulating The Regioselectivity Of Phenylalanine
Aminomutase: New Insights Into The Reaction Mechanism Of
Mio-dependent Enzymes From Structure-guided Directed
Evolution
pdb|4BAB|A Chain A, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|B Chain B, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|C Chain C, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
pdb|4BAB|D Chain D, Redesign Of A Phenylalanine Aminomutase Into A
Beta-phenylalanine Ammonia Lyase
Length = 705
Score = 27.7 bits (60), Expect = 2.0, Method: Composition-based stats.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 87 KFEPKYRLIRNGLDTKVEKSRKQLKERKNRAK 118
KF P YR +R LDT V +R++ +++ K
Sbjct: 642 KFLPFYRFVREELDTGVMSARREQTPQEDVQK 673
>pdb|4ASI|A Chain A, Crystal Structure Of Human Acaca C-Terminal Domain
pdb|4ASI|B Chain B, Crystal Structure Of Human Acaca C-Terminal Domain
pdb|4ASI|C Chain C, Crystal Structure Of Human Acaca C-Terminal Domain
pdb|4ASI|D Chain D, Crystal Structure Of Human Acaca C-Terminal Domain
pdb|4ASI|E Chain E, Crystal Structure Of Human Acaca C-Terminal Domain
pdb|4ASI|F Chain F, Crystal Structure Of Human Acaca C-Terminal Domain
Length = 769
Score = 27.3 bits (59), Expect = 3.0, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 4 TKAVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYE 51
T ++ RK + N+L R++F+I + H + V A+L + RM E
Sbjct: 584 TPELSTAERKELENKLKEREEFLIPIYH--QVAVQFADLHDTPGRMQE 629
>pdb|1QDL|A Chain A, The Crystal Structure Of Anthranilate Synthase From
Sulfolobus Solfataricus
Length = 422
Score = 26.2 bits (56), Expect = 5.7, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 54 DPNAIFVFKFRTHFGGGK----STGFGLIYDSVENAKKFEPKYRL 94
D NA F RT F + G G++YDS ++ FE +++L
Sbjct: 368 DGNAEFAIAIRTAFLNKELLRIHAGAGIVYDSNPESEYFETEHKL 412
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 26.2 bits (56), Expect = 6.0, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 23 KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTG 74
++ + D+LH R ++SK + + LA Y P+A+ + + G G + G
Sbjct: 805 RETINDILH-NRVDISKLIISKTLAPNYTNPQPHAVLAERMKRREGVGPNVG 855
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 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,263,308
Number of Sequences: 62578
Number of extensions: 127821
Number of successful extensions: 481
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 455
Number of HSP's gapped (non-prelim): 31
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)