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= psy1295
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 207 bits (527), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 100/126 (79%), Positives = 108/126 (85%)
Query: 12 EPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEP 71
E VNPKAYPLAD LT K+L LVQQ+ NYKQLRKGANEATKTLNRG+SEFIV+AADAEP
Sbjct: 19 EADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEP 78
Query: 72 LEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXXXXXX 131
LEI+LHLPLLCEDKNVPYVFVRSKQALGRACGVSRP+IACSVT+ EGSQLK
Sbjct: 79 LEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQS 138
Query: 132 XERLLI 137
ERLL+
Sbjct: 139 IERLLV 144
>pdb|2OZB|A Chain A, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|2OZB|D Chain D, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|3SIU|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIU|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIV|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|G Chain G, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|J Chain J, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
Length = 130
Score = 207 bits (526), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 100/126 (79%), Positives = 108/126 (85%)
Query: 12 EPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEP 71
E VNPKAYPLAD LT K+L LVQQ+ NYKQLRKGANEATKTLNRG+SEFIV+AADAEP
Sbjct: 5 EADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEP 64
Query: 72 LEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXXXXXX 131
LEI+LHLPLLCEDKNVPYVFVRSKQALGRACGVSRP+IACSVT+ EGSQLK
Sbjct: 65 LEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQS 124
Query: 132 XERLLI 137
ERLL+
Sbjct: 125 IERLLV 130
>pdb|1E7K|A Chain A, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
pdb|1E7K|B Chain B, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
Length = 128
Score = 207 bits (526), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 100/126 (79%), Positives = 108/126 (85%)
Query: 12 EPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEP 71
E VNPKAYPLAD LT K+L LVQQ+ NYKQLRKGANEATKTLNRG+SEFIV+AADAEP
Sbjct: 3 EADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEP 62
Query: 72 LEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXXXXXX 131
LEI+LHLPLLCEDKNVPYVFVRSKQALGRACGVSRP+IACSVT+ EGSQLK
Sbjct: 63 LEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQS 122
Query: 132 XERLLI 137
ERLL+
Sbjct: 123 IERLLV 128
>pdb|1ZWZ|A Chain A, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
pdb|1ZWZ|B Chain B, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
Length = 126
Score = 175 bits (443), Expect = 7e-45, Method: Compositional matrix adjust.
Identities = 84/124 (67%), Positives = 100/124 (80%)
Query: 14 AVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLE 73
A NPKA+PLAD ALT +IL +VQQA N +QL+KGANEATKTLNRG+SEFI++AAD EP+E
Sbjct: 3 APNPKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIE 62
Query: 74 IVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXXXXXXXE 133
I+LHLPLLCEDKNVPYVFV S+ ALGRACGVSRP+IA S+T ++ S +K E
Sbjct: 63 ILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQIYAVKDKIE 122
Query: 134 RLLI 137
LLI
Sbjct: 123 TLLI 126
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 175 bits (443), Expect = 8e-45, Method: Compositional matrix adjust.
Identities = 84/124 (67%), Positives = 100/124 (80%)
Query: 14 AVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLE 73
A NPKA+PLAD ALT +IL +VQQA N +QL+KGANEATKTLNRG+SEFI++AAD EP+E
Sbjct: 3 APNPKAFPLADAALTQQILDVVQQAANLRQLKKGANEATKTLNRGISEFIIMAADCEPIE 62
Query: 74 IVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXXXXXXXE 133
I+LHLPLLCEDKNVPYVFV S+ ALGRACGVSRP+IA S+T ++ S +K E
Sbjct: 63 ILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQIYAVKDKIE 122
Query: 134 RLLI 137
LLI
Sbjct: 123 TLLI 126
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 174 bits (441), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 82/130 (63%), Positives = 101/130 (77%)
Query: 8 QTNEEPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAA 67
+ +E+ NPKA+PLA L KI++LVQQA NYKQLRKGANEATK LNRG++E ++LAA
Sbjct: 6 EASEDTGFNPKAFPLASPDLNNKIINLVQQACNYKQLRKGANEATKALNRGIAEIVLLAA 65
Query: 68 DAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGSQLKPXXXX 127
DAEPLEI+LHLPL+CEDKN PYVFVRSK ALGRACGVSRP+IA ++T +GS L
Sbjct: 66 DAEPLEILLHLPLVCEDKNTPYVFVRSKVALGRACGVSRPVIAAAITSKDGSSLSSQITE 125
Query: 128 XXXXXERLLI 137
E++L+
Sbjct: 126 LKDQIEQILV 135
>pdb|3O85|A Chain A, Giardia Lamblia 15.5kd Rna Binding Protein
pdb|3O85|B Chain B, Giardia Lamblia 15.5kd Rna Binding Protein
Length = 122
Score = 112 bits (281), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 53/99 (53%), Positives = 76/99 (76%)
Query: 15 VNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEI 74
++P+A P A+ L+ ++L+LV+ + + +++GANEA K +NRG +E +++AADA+P+EI
Sbjct: 3 IDPRAIPFANEELSLELLNLVKHGASLQAIKRGANEALKQVNRGKAELVIIAADADPIEI 62
Query: 75 VLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSV 113
VLHLPL CEDK VPYVF+ SK ALGRAC VS P I S+
Sbjct: 63 VLHLPLACEDKGVPYVFIGSKNALGRACNVSVPTIVASI 101
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 92.8 bits (229), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 45/119 (37%), Positives = 74/119 (62%), Gaps = 18/119 (15%)
Query: 1 MSTFLYFQTNEEPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLS 60
M+ ++ F+ EE + ++L V +A +Q++KGANE TK + RG++
Sbjct: 1 MAVYVKFKVPEE--------------IQKELLDAVAKA---QQIKKGANEVTKAVERGIA 43
Query: 61 EFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVTVDEGS 119
+ +++A D +P E+V HLP LCE+K +PY +V SKQ LG+A GVSRP + ++ ++EG
Sbjct: 44 KLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGVSRPASSVAI-INEGD 101
>pdb|1RLG|A Chain A, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
pdb|1RLG|B Chain B, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
Length = 119
Score = 92.8 bits (229), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 42/93 (45%), Positives = 64/93 (68%), Gaps = 1/93 (1%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
+ + LSL+++ +++KG NE TK + RGL++ + +A D +P EIV HLPLLCE+KN
Sbjct: 11 MQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKN 70
Query: 87 VPYVFVRSKQALGRACGVSRPIIACSVTVDEGS 119
VPY++V+SK LGRA G+ P A + ++EG
Sbjct: 71 VPYIYVKSKNDLGRAVGIEVP-CASAAIINEGE 102
>pdb|3ID5|C Chain C, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3ID5|G Chain G, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3PLA|C Chain C, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|D Chain D, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|L Chain L, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
Length = 130
Score = 91.3 bits (225), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 38/78 (48%), Positives = 57/78 (73%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K+L V++A +++KG NE TK + RG ++ +++A D +P EIV HLPLLC++K
Sbjct: 18 LADKVLEAVRKAKESGKIKKGTNETTKAVERGQAKLVIIAEDVQPEEIVAHLPLLCDEKK 77
Query: 87 VPYVFVRSKQALGRACGV 104
+PYV+V SK+ALG ACG+
Sbjct: 78 IPYVYVSSKKALGEACGL 95
>pdb|2FC3|A Chain A, Crystal Structure Of The Extremely Thermostable Aeropyrum
Pernix L7ae Multifunctional Protein
Length = 124
Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 41/91 (45%), Positives = 61/91 (67%), Gaps = 2/91 (2%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K V++A +++KG NE TK + RGL++ +V+A D +P EIV+HLPLLC++K
Sbjct: 12 LAEKAYEAVKRARETGRIKKGTNETTKAVERGLAKLVVIAEDVDPPEIVMHLPLLCDEKK 71
Query: 87 VPYVFVRSKQALGRACGVSRPIIACSVTVDE 117
+PYV+V SK+ LG A G+ + A SV + E
Sbjct: 72 IPYVYVPSKKRLGEAAGIE--VAAASVAIIE 100
>pdb|1RA4|A Chain A, Crystal Structure Of The Methanococcus Jannaschii L7ae
Protein
pdb|1XBI|A Chain A, High Resolution Structure Of Methanocaldococcus Jannaschii
L7ae
Length = 120
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 43/120 (35%), Positives = 72/120 (60%), Gaps = 20/120 (16%)
Query: 1 MSTFLYFQTNEEPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLS 60
M+ ++ F+ EE + ++L V +A ++++KGANE TK + RG++
Sbjct: 4 MAVYVKFKVPEE--------------IQKELLDAVAKA---QKIKKGANEVTKAVERGIA 46
Query: 61 EFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVT-VDEGS 119
+ +++A D +P E+V HLP LCE+K +PY +V SKQ LG+A G+ + A SV ++EG
Sbjct: 47 KLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLE--VAASSVAIINEGD 104
>pdb|1SDS|A Chain A, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|B Chain B, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|C Chain C, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
Length = 117
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 43/120 (35%), Positives = 72/120 (60%), Gaps = 20/120 (16%)
Query: 1 MSTFLYFQTNEEPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLS 60
M+ ++ F+ EE + ++L V +A ++++KGANE TK + RG++
Sbjct: 1 MAVYVKFKVPEE--------------IQKELLDAVAKA---QKIKKGANEVTKAVERGIA 43
Query: 61 EFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSRPIIACSVT-VDEGS 119
+ +++A D +P E+V HLP LCE+K +PY +V SKQ LG+A G+ + A SV ++EG
Sbjct: 44 KLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLE--VAASSVAIINEGD 101
>pdb|2LBX|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P
Length = 121
Score = 79.0 bits (193), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K+L V++A K +++G E K L +G +V+A D P +++ H+P+LCED +
Sbjct: 4 LNKKVLKTVKKASKAKNVKRGVKEVVKALRKGEKGLVVIAGDISPADVISHIPVLCEDHS 63
Query: 87 VPYVFVRSKQALGRACGVSRP 107
VPY+F+ SKQ LG A RP
Sbjct: 64 VPYIFIPSKQDLGAAGATKRP 84
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 78.6 bits (192), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K+L V++A K +++G E K L +G +V+A D P +++ H+P+LCED +
Sbjct: 4 LNKKVLKTVKKASKAKNVKRGVKEVVKALRKGEKGLVVIAGDIWPADVISHIPVLCEDHS 63
Query: 87 VPYVFVRSKQALGRACGVSRP 107
VPY+F+ SKQ LG A RP
Sbjct: 64 VPYIFIPSKQDLGAAGATKRP 84
>pdb|1PXW|A Chain A, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
pdb|1PXW|B Chain B, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
Length = 128
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 20 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 79
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 80 IPYIYVPSKKELG 92
>pdb|3LWO|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
CONTAINING 5BRU
pdb|3LWP|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
CONTAINING 5BRDU
pdb|3LWQ|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
CONTAINING 3MU
pdb|3LWR|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
CONTAINING 4SU
pdb|3LWV|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA
CONTAINING 2'- Deoxyuridine
pdb|3J20|3 Chain 3, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|4 Chain 4, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 123
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 15 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 74
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 75 IPYIYVPSKKELG 87
>pdb|3NMU|C Chain C, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|G Chain G, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVI|B Chain B, Structure Of N-Terminal Truncated Nop5658 BOUND WITH
L7AE AND BOX CD Rna
pdb|3NVI|D Chain D, Structure Of N-Terminal Truncated Nop5658 BOUND WITH
L7AE AND BOX CD Rna
pdb|3NVK|E Chain E, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|H Chain H, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 129
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 21 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 80
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 81 IPYIYVPSKKELG 93
>pdb|2HVY|D Chain D, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|D Chain D, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA
RNP FROM Pyrococcus Furiosus
pdb|3HAY|D Chain D, Crystal Structure Of A Substrate-Bound Full HACA RNP
FROM Pyrococcus Furiosus
Length = 130
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 16 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 75
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 76 IPYIYVPSKKELG 88
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p
Of P.Horikoshii Ribonuclease P
Length = 124
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 16 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 75
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 76 IPYIYVPSKKELG 88
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein
Pseudouridine Synthase Bound To A Substrate Rna
Length = 120
Score = 77.4 bits (189), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L K L V+ A + ++RKG NE TK + RG ++ +++A D +P EIV HLP LCE+K
Sbjct: 13 LAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKE 72
Query: 87 VPYVFVRSKQALG 99
+PY++V SK+ LG
Sbjct: 73 IPYIYVPSKKELG 85
>pdb|1S72|F Chain F, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|F Chain F, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|F Chain F, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|F Chain F, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|F Chain F, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|F Chain F, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|F Chain F, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|F Chain F, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|F Chain F, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|F Chain F, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|F Chain F, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|F Chain F, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|F Chain F, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|F Chain F, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|F Chain F, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|F Chain F, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|F Chain F, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|F Chain F, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|F Chain F, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|F Chain F, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|F Chain F, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|F Chain F, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|F Chain F, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|F Chain F, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|F Chain F, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|F Chain F, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|F Chain F, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|F Chain F, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|F Chain F, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|F Chain F, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|F Chain F, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|F Chain F, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|F Chain F, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 120
Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 53/88 (60%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L L ++ A + ++KG NE TK++ RG +E + +A D +P EIV+H+P L ++K
Sbjct: 13 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 72
Query: 87 VPYVFVRSKQALGRACGVSRPIIACSVT 114
VP++FV + LG A G+ A +VT
Sbjct: 73 VPFIFVEQQDDLGHAAGLEVGSAAAAVT 100
>pdb|3G4S|F Chain F, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|F Chain F, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|F Chain F, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
Length = 119
Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 53/88 (60%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L L ++ A + ++KG NE TK++ RG +E + +A D +P EIV+H+P L ++K
Sbjct: 12 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 71
Query: 87 VPYVFVRSKQALGRACGVSRPIIACSVT 114
VP++FV + LG A G+ A +VT
Sbjct: 72 VPFIFVEQQDDLGHAAGLEVGSAAAAVT 99
>pdb|1FFK|E Chain E, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|F Chain F, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|F Chain F, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|H Chain H, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|H Chain H, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|H Chain H, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|H Chain H, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|H Chain H, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|H Chain H, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|H Chain H, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|H Chain H, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|H Chain H, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|H Chain H, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|H Chain H, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|H Chain H, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|H Chain H, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|F Chain F, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|F Chain F, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|F Chain F, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|F Chain F, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|F Chain F, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 119
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 49/79 (62%)
Query: 27 LTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
L L ++ A + ++KG NE TK++ RG +E + +A D +P EIV+H+P L ++K
Sbjct: 12 LEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKG 71
Query: 87 VPYVFVRSKQALGRACGVS 105
VP++FV + LG A G+
Sbjct: 72 VPFIFVEQQDDLGHAAGLE 90
>pdb|4A17|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|F Chain F, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 255
Score = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGR 100
L+ G N T + ++ +V+A D +P+E+V+ LP LC +VP+ FV+ K ALG+
Sbjct: 125 LKYGLNHITTLIENKQAKLVVIAHDVDPIELVIFLPQLCRKNDVPFAFVKGKAALGK 181
>pdb|3ZF7|XX Chain x, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 276
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 47 GANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSR 106
G E T+T+ + + +++A + +P+E+VL +P LC +PY V+ K LG A G R
Sbjct: 148 GLQEVTRTIEKKTARLVLIANNVDPIELVLWMPTLCRANKIPYAIVKDKARLGDAIG--R 205
Query: 107 PIIACSVTVD 116
C D
Sbjct: 206 KTATCVAFTD 215
>pdb|3IZR|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 258
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 47 GANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSR 106
G N T + + ++ +V+A D +P+E+V+ LP LC VPY V+ K LG
Sbjct: 131 GLNHVTYLIEQSKAQLVVIAHDVDPIELVVWLPALCRKMEVPYCIVKGKARLGSIVHKKT 190
Query: 107 PIIACSVTVDEGSQL 121
+ C TV +L
Sbjct: 191 ASVLCLTTVKNEDKL 205
>pdb|2ZKR|FF Chain f, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 266
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 32/56 (57%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALG 99
LR G N T + ++ +V+A D +P+E+V+ LP LC VPY ++ K LG
Sbjct: 136 LRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLG 191
>pdb|3JYW|G Chain G, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 113
Score = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALG 99
++ G N + ++ +++A D +P+E+V+ LP LC+ VPY V+ K LG
Sbjct: 26 VKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLG 81
>pdb|1S1I|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, 1s1i, Contains 60s Subunit. The 40s Ribosomal
Subunit Is In File 1s1h
Length = 119
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALG 99
++ G N + ++ +++A D +P+E+V+ LP LC+ VPY V+ K LG
Sbjct: 31 VKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLG 86
>pdb|3IZS|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|G Chain G, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 256
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALG 99
++ G N + ++ +++A D +P+E+V+ LP LC+ VPY V+ K LG
Sbjct: 132 VKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLG 187
>pdb|3V7E|A Chain A, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
pdb|3V7E|B Chain B, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
Length = 82
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 47 GANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACGV 104
G + K L RG + +V+A DA+P+ + + L ED+ + V S + LG+ACG+
Sbjct: 15 GTKQTVKALKRGSVKEVVVAKDADPI-LTSSVVSLAEDQGISVSMVESMKKLGKACGI 71
>pdb|3ON1|A Chain A, The Structure Of A Protein With Unknown Function From
Bacillus Halodurans C
Length = 101
Score = 33.9 bits (76), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 1/80 (1%)
Query: 30 KILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPY 89
K LSL+ A +QL G + K + G ++L++DA + L C +P
Sbjct: 5 KWLSLLGLAARARQLLTGEEQVVKAVQNGQVTLVILSSDA-GIHTKKKLLDKCGSYQIPV 63
Query: 90 VFVRSKQALGRACGVSRPII 109
V ++Q LGRA G ++
Sbjct: 64 KVVGNRQXLGRAIGKHERVV 83
>pdb|3U5C|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|M Chain M, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 143
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 34 LVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCED--KNVPYVF 91
+++ AL + L +G E+TK L RG + +VL + I+ + L D VP +
Sbjct: 31 VLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLANDPENKVPLIK 90
Query: 92 VRSKQALGRACGVSR 106
V + LG G+ +
Sbjct: 91 VADAKQLGEWAGLGK 105
>pdb|3ZEY|F Chain F, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 144
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 42/95 (44%)
Query: 12 EPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADAEP 71
EPAV +L + ++ +A L G +E T+ L+R + VLA D E
Sbjct: 14 EPAVIDAVADAMPDSLEDALRIVLMKARETNGLICGLSEVTRALDRRTAHLCVLADDCED 73
Query: 72 LEIVLHLPLLCEDKNVPYVFVRSKQALGRACGVSR 106
E + L + N+ V + ++ L + G++R
Sbjct: 74 EEYKKLVTALAKQNNIDLVSMDEREKLAQWAGLTR 108
>pdb|3H5Q|A Chain A, Crystal Structure Of A Putative Pyrimidine-Nucleoside
Phosphorylase From Staphylococcus Aureus
Length = 436
Score = 28.5 bits (62), Expect = 1.3, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 39/97 (40%), Gaps = 7/97 (7%)
Query: 10 NEEPAVNPKAYPLADTALTTKILSLVQQALNYKQLRKGANEATKTLNRGLSEFIVLAADA 69
N PA + K Y L D T + L+ ++ K++ GA+ + G F DA
Sbjct: 159 NLTPA-DKKLYALRDVTGTVNSIPLIASSIXSKKIAAGADAIVLDVKTGSGAFXKTLEDA 217
Query: 70 EPLEIVLHLPLLCED---KNVPYVFVRSKQALGRACG 103
E L H + + +N + Q LGRA G
Sbjct: 218 EALA---HAXVRIGNNVGRNTXAIISDXNQPLGRAIG 251
>pdb|2XZM|U Chain U, 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|U Chain U, 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 = 126
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 28/60 (46%)
Query: 44 LRKGANEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALGRACG 103
+ KG +E +T+ + F+ +A D + V + LC + YV V + +LG G
Sbjct: 25 ISKGLHEVLRTIEAKQALFVCVAEDCDQGNYVKLVKALCAKNEIKYVSVPKRASLGEYLG 84
>pdb|1KTE|A Chain A, Crystal Structure Of Thioltransferase At 2.2 Angstrom
Resolution
Length = 105
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 55 LNRGLSEFIVLAADAEPLEIVLHLPLLCEDKNVPYVFVRSKQALG 99
GL EF+ + A ++ EI +L L + VP VF+ K+ +G
Sbjct: 37 FKEGLLEFVDITATSDTNEIQDYLQQLTGARTVPRVFI-GKECIG 80
>pdb|2WG3|C Chain C, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Desert Hedgehog Without
Calcium
pdb|2WG3|D Chain D, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Desert Hedgehog Without
Calcium
Length = 463
Score = 25.8 bits (55), Expect = 7.4, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 49 NEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
N+ + GL + A D P +I ++L +LC D N
Sbjct: 206 NQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSN 243
>pdb|2WFX|B Chain B, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog In The
Presence Of Calcium
pdb|2WG4|B Chain B, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog Without
Calcium
Length = 457
Score = 25.8 bits (55), Expect = 7.4, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 49 NEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
N+ + GL + A D P +I ++L +LC D N
Sbjct: 206 NQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSN 243
>pdb|2WFT|A Chain A, Crystal Structure Of The Human Hip Ectodomain
pdb|2WFT|B Chain B, Crystal Structure Of The Human Hip Ectodomain
Length = 458
Score = 25.8 bits (55), Expect = 7.4, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 49 NEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
N+ + GL + A D P +I ++L +LC D N
Sbjct: 206 NQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSN 243
>pdb|3HO3|A Chain A, Crystal Structure Of Hedgehog-interacting Protein (hhip)
pdb|3HO5|A Chain A, Crystal Structure Of Hedgehog-interacting Protein (hhip)
And Sonic Hedgehog (shh) Complex
pdb|3HO5|B Chain B, Crystal Structure Of Hedgehog-interacting Protein (hhip)
And Sonic Hedgehog (shh) Complex
Length = 481
Score = 25.8 bits (55), Expect = 7.4, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 49 NEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
N+ + GL + A D P +I ++L +LC D N
Sbjct: 227 NQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSN 264
>pdb|3HO4|A Chain A, Crystal Structure Of Hedgehog-Interacting Protein (Hhip)
pdb|3HO4|B Chain B, Crystal Structure Of Hedgehog-Interacting Protein (Hhip)
Length = 481
Score = 25.8 bits (55), Expect = 7.6, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 49 NEATKTLNRGLSEFIVLAADAEPLEIVLHLPLLCEDKN 86
N+ + GL + A D P +I ++L +LC D N
Sbjct: 227 NQPPEVFAHGLHDPGRCAVDRHPTDININLTILCSDSN 264
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
0.318 0.134 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,209,372
Number of Sequences: 62578
Number of extensions: 102918
Number of successful extensions: 246
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 202
Number of HSP's gapped (non-prelim): 44
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)