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= psy2768
(96 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 3/94 (3%)
Query: 2 AQYLIFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
AQ I+ K++EE F +EV+L + VP+S GR+IGKGG+ V ELQ T + + +P
Sbjct: 63 AQGRIYGKLKEENFFGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
Query: 62 SFNEEETN---VHIVGSFFSVQETLKGCPNIVDQ 92
+E + V I+G F++ Q + +I+ Q
Sbjct: 123 DQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQ 156
Score = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 24/34 (70%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+++ +P+ VG IIGK GQ++++L R + IK+
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKI 38
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 2/63 (3%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF--NEEETNVHIVGSFFSVQE 81
+T+ LVVP+SQ G +IGKGG ++E++ STG+ +++ N E + I G S+ E
Sbjct: 89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIE 148
Query: 82 TLK 84
+K
Sbjct: 149 CVK 151
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 27/38 (71%)
Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
V LTI L++ +VG IIGK G++V++++ +G+ I +
Sbjct: 3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI 40
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM
WITH 25 NT RNA Hairpin
Length = 178
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
+++++PS G IIGKGGQ + +LQ+ TG+ IKL S
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKS 44
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL---PNSFNEEETNVHIVG 74
++++VP+S G IIGKGG V+ + +G+ ++L P+ N + V + G
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG 157
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM
WITH 25NT RNA Hairpin
Length = 178
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 27/37 (72%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
+++++PS G IIGKGGQ + +LQ+ TG+ IKL S
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKS 44
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL---PNSFNEEETNVHIVG 74
++++VP+S G IIGKGG V+ + +G+ ++L P+ N + V + G
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIXEQSGAWVQLSQKPDGINLQNRVVTVSG 157
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGSFFSVQET 82
+T E VP VG IIG+GG+ + ++Q+ +G +++ P+S E +V + G+ SVQ+
Sbjct: 16 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKA 75
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein
1
Length = 92
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL-PNSFNEEETNVHIVGSFFSVQET 82
+T E VP VG IIG+GG+ + +Q+ +G I++ P+S E + + G+ SVQ
Sbjct: 15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 74
Query: 83 LKGCPNIVDQ 92
+ IV++
Sbjct: 75 KRLLDQIVEK 84
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 10/70 (14%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG-SMIKLPNSFNEEETNV----HIVGSFFSVQE 81
E+++P+ + G +IGKGG+ +++LQ G MI + + + TNV I+G + VQ+
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG--SQNTNVDKPLRIIGDPYKVQQ 74
Query: 82 TLKGCPNIVD 91
C ++D
Sbjct: 75 A---CEMVMD 81
>pdb|1ZZI|A Chain A, Crystal Structure Analysis Of The Third Kh Domain Of
Hnrnp K In Complex With Ssdna
pdb|1ZZI|B Chain B, Crystal Structure Analysis Of The Third Kh Domain Of
Hnrnp K In Complex With Ssdna
pdb|1ZZJ|A Chain A, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|B Chain B, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZJ|C Chain C, Structure Of The Third Kh Domain Of Hnrnp K In Complex
With 15-Mer Ssdna
pdb|1ZZK|A Chain A, Crystal Structure Of The Third Kh Domain Of Hnrnp K At
0.95a Resolution
Length = 82
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQET 82
+T ++ +P G IIGKGGQ +++++ +G+ IK+ E+ + I G+ +Q
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 66
Query: 83 LKGCPNIVDQPS 94
N V Q S
Sbjct: 67 QYLLQNSVKQYS 78
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQET 82
+T ++ +P G IIGKGGQ +++++ +G+ IK+ E+ + I G+ +Q
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73
Query: 83 LKGCPNIVDQPS 94
N V Q S
Sbjct: 74 QYLLQNSVKQYS 85
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc
Binding Protein
Length = 82
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSV 79
T EL +P++ +G IIG+ G N+ E+++ +G+ IK+ N V I GS S+
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASI 62
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh
Domains Of Ksrp
Length = 164
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 10/70 (14%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG-SMIKLPNSFNEEETNV----HIVGSFFSVQE 81
E+++P+ + G +IGKGG+ +++LQ G MI + + + TNV I+G + VQ+
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG--SQNTNVDKPLRIIGDPYKVQQ 62
Query: 82 TLKGCPNIVD 91
C ++D
Sbjct: 63 A---CEMVMD 69
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTG---SMIKLPNSFNEEETNVHIVGSFFSVQET 82
E+++P+S+ G +IGKGG+ +++LQ G MI+ + + I G + VQ+
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQA 76
>pdb|1DTJ|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|C Chain C, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
pdb|1DTJ|D Chain D, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain
Length = 76
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK-------LPNSFNEEETNVHIVGSFFS 78
+E+ VP + VG I+GKGG+ + E Q TG+ I+ LP + N V I GS +
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNR---RVTITGSPAA 61
Query: 79 VQ 80
Q
Sbjct: 62 TQ 63
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 23/31 (74%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMI 57
+L VP VGRIIG+GG+ +R + +++G+ I
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKI 48
>pdb|2P2R|A Chain A, Crystal Structure Of The Third Kh Domain Of Human
Poly(C)- Binding Protein-2 In Complex With C-Rich
Strand Of Human Telomeric Dna
Length = 76
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSV 79
EL +P+ +G IIG+ G + E+++ +G+ IK+ N + V I GS S+
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASI 61
>pdb|1EC6|A Chain A, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
pdb|1EC6|B Chain B, Crystal Structure Of Nova-2 Kh3 K-Homology Rna-Binding
Domain Bound To 20-Mer Rna Hairpin
Length = 87
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK-------LPNSFNEEETNVHIVGSFFS 78
+E+ VP + VG I+GKGG+ + E Q TG+ I+ LP + N V I GS +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNR---RVTITGSPAA 61
Query: 79 VQ 80
Q
Sbjct: 62 TQ 63
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 10/62 (16%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIK-------LPNSFNEEETNVHIVGSFFS 78
+E+ VP + VG I+GKGG+ + E Q TG I+ LP + N + V I G+ +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRK---VTITGTPAA 61
Query: 79 VQ 80
Q
Sbjct: 62 TQ 63
>pdb|1J4W|A Chain A, Complex Of The Kh3 And Kh4 Domains Of Fbp With A
Single_stranded 29mer Dna Oligonucleotide From The Fuse
Element Of The C-Myc Oncogene
Length = 174
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 9/65 (13%)
Query: 28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLP-NSFNEEETNVHIVGSFFSVQETLKGC 86
+VP+ + G IIGKGG+ ++ + + +G+ I+L N + N+ + T++G
Sbjct: 108 FIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLF--------TIRGT 159
Query: 87 PNIVD 91
P +D
Sbjct: 160 PQQID 164
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSF-NEEETNVHIVGSFFSVQET 82
+T ++ +P IIGKGGQ +++++ +G+ IK+ E+ + I G+ +Q
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73
Query: 83 LKGCPNIVDQPS 94
N V Q S
Sbjct: 74 QYLLQNSVKQYS 85
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 23/30 (76%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+P+ + G +IG+GG+NV+ + + TG+ +++
Sbjct: 13 IPTHKCGLVIGRGGENVKAINQQTGAFVEI 42
>pdb|3VKE|A Chain A, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|B Chain B, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|C Chain C, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
pdb|3VKE|D Chain D, Contribution Of The First K-Homology Domain Of
Poly(C)-Binding Protein 1 To Its Affinity And
Specificity For C-Rich Oligonucleotides
Length = 76
Score = 32.0 bits (71), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
LTI L++ +VG IIGK G++V+ ++ +G+ I +
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI 38
>pdb|2AXY|A Chain A, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|B Chain B, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|C Chain C, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2AXY|D Chain D, Crystal Structure Of Kh1 Domain Of Human Poly(C)-Binding
Protein-2 With C-Rich Strand Of Human Telomeric Dna
pdb|2PQU|A Chain A, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|B Chain B, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|C Chain C, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PQU|D Chain D, Crystal Structure Of Kh1 Domain Of Human Pcbp2 Complexed
To Single- Stranded 12-Mer Telomeric Dna
pdb|2PY9|A Chain A, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|B Chain B, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|C Chain C, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
pdb|2PY9|D Chain D, Protein-Rna Interaction Involving Kh1 Domain From Human
Poly(C)-Binding Protein-2
Length = 73
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 22 VRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
V LTI L+ +VG IIGK G++V++ + +G+ I +
Sbjct: 3 VTLTIRLLXHGKEVGSIIGKKGESVKKXREESGARINI 40
>pdb|1ZTG|A Chain A, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|B Chain B, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|C Chain C, Human Alpha Polyc Binding Protein Kh1
pdb|1ZTG|D Chain D, Human Alpha Polyc Binding Protein Kh1
Length = 74
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
LTI L++ +VG IIGK G++V+ ++ +G+ I +
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINI 38
>pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima
Length = 344
Score = 28.9 bits (63), Expect = 0.69, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFN 64
++VP +Q+ IGKGGQN R + TG I + N
Sbjct: 307 VLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMN 343
>pdb|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A
Structure-Based Role Of The N-Terminal Domain
Length = 369
Score = 28.9 bits (63), Expect = 0.73, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 28 LVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
++VP +Q+ IGKGGQN R + TG I +
Sbjct: 332 VLVPPTQLSLAIGKGGQNARLAAKLTGWKIDI 363
>pdb|3U1K|A Chain A, Crystal Structure Of Human Pnpase
pdb|3U1K|C Chain C, Crystal Structure Of Human Pnpase
pdb|3U1K|B Chain B, Crystal Structure Of Human Pnpase
pdb|3U1K|D Chain D, Crystal Structure Of Human Pnpase
Length = 630
Score = 28.9 bits (63), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMI 57
VP S+ + +G GG N+++LQ TG I
Sbjct: 573 VPLSKRAKFVGPGGYNLKKLQAETGVTI 600
>pdb|1K0R|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Nusa
pdb|1K0R|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Nusa
Length = 366
Score = 28.5 bits (62), Expect = 0.90, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 20/40 (50%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
D+ +VVP Q+ IGK GQN R R TG I +
Sbjct: 303 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDI 342
>pdb|2ASB|A Chain A, Structure Of A Mycobacterium Tuberculosis Nusa-Rna Complex
pdb|2ATW|A Chain A, Structure Of A Mycobacterium Tuberculosis Nusa-Rna Complex
pdb|2ATW|C Chain C, Structure Of A Mycobacterium Tuberculosis Nusa-Rna Complex
Length = 251
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%)
Query: 20 DEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
D+ +VVP Q+ IGK GQN R R TG I +
Sbjct: 180 DQTARAARVVVPDFQLSLAIGKEGQNARLAARLTGWRIDI 219
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 9/30 (30%), Positives = 21/30 (70%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+P+ ++ +IG GG+ +RE+ +TG+ + +
Sbjct: 567 IPTDKIREVIGSGGKVIREIVATTGAKVDI 596
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 9/30 (30%), Positives = 21/30 (70%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+P+ ++ +IG GG+ +RE+ +TG+ + +
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDI 605
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 9/30 (30%), Positives = 21/30 (70%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
+P+ ++ +IG GG+ +RE+ +TG+ + +
Sbjct: 576 IPTDKIREVIGSGGKVIREIVATTGAKVDI 605
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 28.1 bits (61), Expect = 1.4, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 6 IFEKMREEGLFAGADEVRLTIELVVPSSQVGRIIGKGGQNVRELQRSTG 54
I E + EE +T E+++ + + G +IGK G RE+ ++TG
Sbjct: 80 IHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTG 128
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring
Finger And Kh Domain Containing Protein 1
Length = 83
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 25 TIELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE 65
TI++ VP VG ++G G ++ +Q+ T + I P E
Sbjct: 11 TIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKE 51
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 26 IELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKLPN 61
I + +P ++G +IG Q + ++Q TG+ I + +
Sbjct: 600 ITVKIPVDKIGEVIGPKRQXINQIQEDTGAEITIED 635
>pdb|3J20|C Chain C, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 210
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 20/28 (71%)
Query: 24 LTIELVVPSSQVGRIIGKGGQNVRELQR 51
L ++++ ++ G +IG+GG+ +REL R
Sbjct: 40 LGTKVIIFAANPGYVIGRGGRRIRELTR 67
>pdb|1PNS|C Chain C, Crystal Structure Of A Streptomycin Dependent Ribosome
From E. Coli, 30s Subunit Of 70s Ribosome. This File,
1pns, Contains The 30s Subunit, Two Trnas, And One Mrna
Molecule. The 50s Ribosomal Subunit Is In File 1pnu.
pdb|1PNX|C Chain C, Crystal Structure Of The Wild Type Ribosome From E. Coli,
30s Subunit Of 70s Ribosome. This File, 1pnx, Contains
Only Molecules Of The 30s Ribosomal Subunit. The 50s
Subunit Is In The Pdb File 1pny.
pdb|1VOQ|C Chain C, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOS|C Chain C, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOV|C Chain C, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOX|C Chain C, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOZ|C Chain C, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|3MR8|C Chain C, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|C Chain C, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s).
pdb|3PYN|C Chain C, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The First 70s Ribosome.
pdb|3PYQ|C Chain C, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The Second 70s
Ribosome.
pdb|3PYS|C Chain C, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The First 70s Ribosome.
pdb|3PYU|C Chain C, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The Second 70s Ribosome
Length = 206
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVR----ELQRSTGSMIKL 59
AD V +T+ + P G +IG+GG+ +R EL + TG + L
Sbjct: 60 ADNVAVTVHVAKP----GVVIGRGGERIRVLREELAKLTGKNVAL 100
>pdb|3FIC|C Chain C, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 30s Subunit
And The Ligands
Length = 207
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVR----ELQRSTGSMIKL 59
AD V +T+ + P G +IG+GG+ +R EL + TG + L
Sbjct: 60 ADNVAVTVHVAKP----GVVIGRGGERIRVLREELAKLTGKNVAL 100
>pdb|1FJG|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin, And Paromomycin
pdb|1HR0|C Chain C, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNW|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1HNZ|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1GIX|F Chain F, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1IBK|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1IBL|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1IBM|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1JGO|F Chain F, The Path Of Messenger Rna Through The Ribosome. This File,
1jgo, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGP|F Chain F, The Path Of Messenger Rna Through The Ribosome. This File,
1jgp, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGQ|F Chain F, The Path Of Messenger Rna Through The Ribosome. This File,
1jgq, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1J5E|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1N32|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The First Codon
Position At The A Site With Paromomycin
pdb|1N33|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The Second Codon
Position At The A Site With Paromomycin
pdb|1N34|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Codon And
Crystallographically Disordered Near-Cognate Transfer
Rna Anticodon Stem-Loop Mismatched At The First Codon
Position
pdb|1N36|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Crystallographically
Disordered Codon And Near-cognate Transfer Rna Anticodon
Stem-loop Mismatched At The Second Codon Position
pdb|1ML5|F Chain F, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1XMO|C Chain C, Crystal Structure Of Mnm5u34t6a37-Trnalysuuu Complexed
With Aag-Mrna In The Decoding Center
pdb|1XMQ|C Chain C, Crystal Structure Of T6a37-Asllysuuu Aaa-Mrna Bound To The
Decoding Center
pdb|1XNQ|C Chain C, Structure Of An Inosine-Adenine Wobble Base Pair Complex
In The Context Of The Decoding Center
pdb|1XNR|C Chain C, Crystal Structure Of An Inosine-Cytosine Wobble Base Pair
In The Context Of The Decoding Center
pdb|1YL4|F Chain F, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. 30s Subunit. The Coordinates For The 50s Subunit
Are In The Pdb Entry 1yl3
pdb|2B64|C Chain C, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|2B9M|C Chain C, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400.
pdb|2B9O|C Chain C, 30s Ribosomal Subunit, Trnas And Mrna From A Crystal
Structure Of The Whole Ribosomal Complex With A Stop
Codon In The A-Site. This File Contains The 30s Subunit,
Trnas And Mrna From A Crystal Structure Of The Whole
Ribosomal Complex With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|2F4V|C Chain C, 30s Ribosome + Designer Antibiotic
pdb|2HHH|C Chain C, Crystal Structure Of Kasugamycin Bound To The 30s
Ribosomal Subunit
pdb|2J00|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 1 Of 4).
This File Contains The 30s Subunit, Mrna, A-, P- And
E-Site Trnas And Paromomycin For Molecule I.
pdb|2J02|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 3 Of 4)
This File Contains The 30s Subunit, Mrna, A-, P- And
E-Site Trnas And Paromomycin For Molecule Ii.
pdb|2HGI|F Chain F, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
Showing How The 16s 3'-End Mimicks Mrna E And P Codons.
This Entry 2hgi Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgj.
pdb|2HGP|F Chain F, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
With Translocated And Rotated Shine-Dalgarno Duplex.
This Entry 2hgp Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgq.
pdb|2HGR|F Chain F, 70s T.Th. Ribosome Functional Complex With Mrna And E- And
P-Site Trnas At 4.5a. This Entry 2hgr Contains 30s
Ribosomal Subunit. The 50s Ribosomal Subunit Can Be
Found In Pdb Entry 2hgu.
pdb|2OW8|DD Chain d, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
Functional Interactions And Rearrangements. This File,
2ow8, Contains The 30s Ribosome Subunit, Two Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File
1vsa.
pdb|2UU9|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-asl With Cmo5u In
Position 34 Bound To An Mrna With A Gug-codon In The
A-site And Paromomycin.
pdb|2UUA|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-Asl With Cmo5u In
Position 34 Bound To An Mrna With A Guc-Codon In The
A-Site And Paromomycin.
pdb|2UUB|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-Asl With Cmo5u In
Position 34 Bound To An Mrna With A Guu-Codon In The
A-Site And Paromomycin.
pdb|2UUC|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Valine-asl With Cmo5u In
Position 34 Bound To An Mrna With A Gua-codon In The
A-site And Paromomycin.
pdb|2UXC|C Chain C, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Ucgu In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2UXB|C Chain C, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Gggu In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2V46|C Chain C, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|C Chain C, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2UXD|C Chain C, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Cggg In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2QNH|DD Chain d, Interactions And Dynamics Of The Shine-Dalgarno Helix In
The 70s Ribosome. This File, 2qnh, Contains The 30s
Ribosome Subunit, Two Trna, And Mrna Molecules. 50s
Ribosome Subunit Is In The File 1vsp.
pdb|2VQE|C Chain C, Modified Uridines With C5-methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-g
Wobble Pairing During Decoding
pdb|2VQF|C Chain C, Modified Uridines With C5-Methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-G
Wobble Pairing During Decoding
pdb|3D5A|C Chain C, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|C Chain C, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3F1E|C Chain C, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|C Chain C, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|2WDG|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule I.
pdb|2WDH|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule Ii.
pdb|2WDK|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule I.
pdb|2WDM|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule Ii.
pdb|2WH1|C Chain C, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|C Chain C, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit.
pdb|3HUW|C Chain C, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
Molecule I.
pdb|3HUY|C Chain C, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 30s Subunit, Mrna, P-Site Trna And Ef-P For
Molecule Ii.
pdb|2WRI|C Chain C, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 1 Of 4).
pdb|2WRK|C Chain C, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 3 Of 4).
pdb|2WRN|C Chain C, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 1 Of 4).
pdb|2WRQ|C Chain C, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 3 Of 4).
pdb|3KIQ|CC Chain c, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 1 Of 4)
pdb|3KIS|CC Chain c, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 3 Of 4)
pdb|3KIU|CC Chain c, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 1 Of 4)
pdb|3KIX|CC Chain c, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 3 Of 4)
pdb|3KNH|C Chain C, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 30s Subunit For Molecule I
pdb|3KNJ|C Chain C, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 30s Subunit For Molecule Ii'
pdb|3KNL|C Chain C, The Structures Of Capreomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule I
pdb|3KNN|C Chain C, The Structures Of Capreomycin Bound To The 70s Ribosome.
This File Contains The 30s Subunit For Molecule Ii
pdb|3I8G|F Chain F, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8g Contains 30s Ribosomal Subnit.The 50s
Ribosomal Can Be Found In Pdb Entry 3i8f. Molecule B In
The Same Asym Unit Is Deposited As 3i8g (30s) And 3i8f
(50s).
pdb|3I8H|F Chain F, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8h Contains 30s Ribosomal Subnit. The 50s
Ribosomal Can Be Found In Pdb Entry 3i8i. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I9B|F Chain F, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9b Contains 30s Ribosomal Subunit Of Molecule B.
The 50s Subunit Can Be Found In Pdb Entry 3i9c. Molecule
A In The S Asymmetric Unit Is Deposited As 3i9d (30s)
And 3i9e (50s)
pdb|3I9D|F Chain F, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9d Contains 30s Ribosomal Subunit Of Molecule A.
The 50s Subunit Can Be Found In Pdb Entry 3i9e. Molecule
B In The S Asymmetric Unit Is Deposited As 3i9b (30s)
And 3i9c (50s)
pdb|2X9R|C Chain C, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|C Chain C, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XFZ|C Chain C, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 1 Of 4)
pdb|2XG1|C Chain C, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 3 Of 4)
pdb|3OTO|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From A Ksga
Mutant Of Thermus Thermophilus (Hb8)
pdb|3OGE|C Chain C, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OGY|C Chain C, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OHC|C Chain C, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHD|C Chain C, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHY|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI0|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI2|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI4|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2XQD|C Chain C, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XSY|C Chain C, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUY|C Chain C, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0U|C Chain C, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0W|C Chain C, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Y|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y10|C Chain C, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y12|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y14|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y16|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y18|C Chain C, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|3ZVO|C Chain C, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3T1H|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aaa-Codon In The A-Site And Paromomycin
pdb|3T1Y|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aag-Codon In The A-Site And Paromomycin
pdb|3UXS|C Chain C, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UXT|C Chain C, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.'
pdb|3TVF|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3TVG|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3UYD|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UYF|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UZ3|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin.
pdb|3UZ4|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin.
pdb|3UZ6|F Chain F, Structure Analysis Of Ribosomal Decoding. This Entry
Contains The 30s Ribosomal Subunit Of The First 70s
Molecule In The Asymmetric Unit For The Cognate Trna-Tyr
Complex
pdb|3UZ7|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZG|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex
pdb|3UZI|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex
pdb|3UZL|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex With Paromomycin
pdb|3UZM|F Chain F, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 30s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-cognate
Trna-tyr Complex With Paromomycin
pdb|4ABR|C Chain C, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4DH9|C Chain C, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHB|C Chain C, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V22|C Chain C, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Rmf Of The 1st Ribosome In The Asu
pdb|3V24|C Chain C, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Rmf Of The 2nd Ribosome In The Asu
pdb|3V26|C Chain C, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Hpf Of The 1st Ribosome In The Asu
pdb|3V28|C Chain C, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Hpf Of The 2nd Ribosome In The Asu
pdb|3V2C|C Chain C, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Yfia Of The 1st Ribosome In The Asu
pdb|3V2E|C Chain C, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Yfia Of The 2nd Ribosome In The Asu
pdb|4AQY|C Chain C, Structure Of Ribosome-Apramycin Complexes
pdb|4DR1|C Chain C, Crystal Structure Of The Apo 30s Ribosomal Subunit From
Thermus Thermophilus (hb8)
pdb|4DR2|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Multiple Copies Of Paromomycin
Molecules Bound
pdb|4DR3|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Streptomycin Bound
pdb|4DR4|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Cognate Transfer Rna
Anticodon Stem-loop And Multiple Copies Of Paromomycin
Molecules Bound
pdb|4DR5|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Crystallographically
Disordered Cognate Transfer Rna Anticodon Stem-loop And
Streptomycin Bound
pdb|4DR6|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Near-cognate Transfer Rna
Anticodon Stem-loop Mismatched At The First Codon
Position And Streptomycin Bound
pdb|4DR7|C Chain C, Crystal Structure Of The Thermus Thermophilus (hb8) 30s
Ribosomal Subunit With Codon, Crystallographically
Disordered Near-cognate Transfer Rna Anticodon Stem-loop
Mismatched At The Second Codon Position, And
Streptomycin Bound
pdb|4G5K|F Chain F, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 30s Subunit Of Molecule A.
pdb|4G5M|F Chain F, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 30s Subunit Of Molecule B.
pdb|4G5T|F Chain F, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 30s Subunit Of Molecule A.
pdb|4G5V|F Chain F, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 30s Subunit Of Molecule B.
pdb|4DUY|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U13c
pdb|4DUZ|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U13c, Bound
With Streptomycin
pdb|4DV0|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U20g
pdb|4DV1|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, U20g, Bound
With Streptomycin
pdb|4DV2|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, C912a
pdb|4DV3|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, C912a, Bound
With Streptomycin
pdb|4DV4|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A914g
pdb|4DV5|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A914g, Bound
With Streptomycin
pdb|4DV6|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A915g
pdb|4DV7|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit With A 16s Rrna Mutation, A915g, Bound
With Streptomycin
Length = 239
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVR----ELQRSTGSMIKL 59
AD V +T+ + P G +IG+GG+ +R EL + TG + L
Sbjct: 61 ADNVAVTVHVAKP----GVVIGRGGERIRVLREELAKLTGKNVAL 101
>pdb|1I94|C Chain C, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I95|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
pdb|1I96|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|C Chain C, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|2E5L|C Chain C, A Snapshot Of The 30s Ribosomal Subunit Capturing Mrna Via
The Shine- Dalgarno Interaction
pdb|2ZM6|C Chain C, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit
Length = 238
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 19 ADEVRLTIELVVPSSQVGRIIGKGGQNVR----ELQRSTGSMIKL 59
AD V +T+ + P G +IG+GG+ +R EL + TG + L
Sbjct: 60 ADNVAVTVHVAKP----GVVIGRGGERIRVLREELAKLTGKNVAL 100
>pdb|3BRZ|A Chain A, Crystal Structure Of The Pseudomonas Putida Toluene
Transporter Todx
pdb|3BS0|A Chain A, Crystal Structure Of The P. Putida Toluene Transporter
Todx
pdb|3BS0|B Chain B, Crystal Structure Of The P. Putida Toluene Transporter
Todx
Length = 439
Score = 26.2 bits (56), Expect = 5.1, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 24 LTIELVVPSSQVGRIIGKG 42
L +EL++PSSQVG + +G
Sbjct: 162 LNLELLLPSSQVGALTAQG 180
>pdb|2E3U|A Chain A, Crystal Structure Analysis Of Dim2p From Pyrococcus
Horikoshii Ot3
pdb|3AEV|B Chain B, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 219
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTGSMIKLPNSFNE 65
+P ++ +IGK GQ +E+++ T + I + + E
Sbjct: 40 IPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGE 75
>pdb|2FFH|A Chain A, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|B Chain B, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
pdb|2FFH|C Chain C, The Signal Sequence Binding Protein Ffh From Thermus
Aquaticus
Length = 425
Score = 26.2 bits (56), Expect = 5.6, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 39/91 (42%), Gaps = 11/91 (12%)
Query: 16 FAGADEVRLTIELVVPSSQVGRIIGKGG-QNVRELQRSTGSMIKLPNS--------FNEE 66
FAG E +E P GRI+G G ++ E R+ G + P S F ++
Sbjct: 269 FAGVSEKPEGLEPFYPERLAGRILGMGDVASLAEKVRAAGLEAEAPKSAKELSLEDFLKQ 328
Query: 67 ETNVHIVGSFFSVQETLKGCPN--IVDQPSI 95
N+ +G F + L G P VD+ +I
Sbjct: 329 MQNLKRLGPFSEILGLLPGVPQGLKVDEKAI 359
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 27 ELVVPSSQVGRIIGKGGQNVRELQRSTGSMIKL 59
E+++ + + G +IGK G +RE+ + G + K+
Sbjct: 105 EVIIEAEKPGLVIGKHGATLREITKQIGWIPKV 137
>pdb|2QND|A Chain A, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
pdb|2QND|B Chain B, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
Length = 144
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 30 VPSSQVGRIIGKGGQNVRELQRSTG 54
VP + VG++IGK G+ ++E+ +G
Sbjct: 73 VPRNLVGKVIGKNGKLIQEIVDKSG 97
>pdb|1TUA|A Chain A, 1.5 A Crystal Structure Of A Protein Of Unknown Function
Ape0754 From Aeropyrum Pernix
Length = 191
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 36 GRIIGKGGQNVRELQRSTGSMIKLPNSFNEEETNVHIVGSF 76
GRIIG+GG+ R ++ T + I N E V I+G +
Sbjct: 110 GRIIGEGGRARRTIEEMTDTYI------NVGEYEVAIIGDY 144
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 25.4 bits (54), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 33 SQVGRIIGKGGQNVRELQRSTGSMIKLPNS 62
++ +IGKGG +R L TG+ I++ +
Sbjct: 569 DKIKDVIGKGGSVIRALTEETGTTIEIEDD 598
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
0.316 0.136 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,780,920
Number of Sequences: 62578
Number of extensions: 99608
Number of successful extensions: 310
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 261
Number of HSP's gapped (non-prelim): 57
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)