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= 003933
(785 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 56/165 (33%), Positives = 83/165 (50%), Gaps = 7/165 (4%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
K+ +P+ G +IGK G TI LQ +GA I++++ D P R I GT+ ++
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 263 EKLINAVIAEA---DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIK 319
I I E A P + + T A QV+I VPN GLIIG+GG T+K
Sbjct: 69 HGFIAEKIREMPQNVAKTEPVSILQPQTTVNPD-RANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 320 GLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364
+ +SGA +Q+ P+G + R+V V+G+ Q A E+I
Sbjct: 128 AIMEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELI 169
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHL-PEGDGSKERIVRVTGDMRQ 356
+++ +P+ G IIG+GG+TI LQ +GA I++ + P G+ ER+ + G +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP---GTTERVCLIQGTIEA 64
Query: 357 IEIAQEMIKE 366
+ I E
Sbjct: 65 LNAVHGFIAE 74
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 56/165 (33%), Positives = 83/165 (50%), Gaps = 7/165 (4%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
K+ +P+ G +IGK G TI LQ +GA I++++ D P R I GT+ ++
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 263 EKLINAVIAEA---DAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIK 319
I I E A P + + T A QV+I VPN GLIIG+GG T+K
Sbjct: 69 HGFIAEKIREXPQNVAKTEPVSILQPQTTVNPD-RANQVKIIVPNSTAGLIIGKGGATVK 127
Query: 320 GLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364
+ +SGA +Q+ P+G + R+V V+G+ Q A E+I
Sbjct: 128 AIXEQSGAWVQL---SQKPDGINLQNRVVTVSGEPEQNRKAVELI 169
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHL-PEGDGSKERIVRVTGDMRQ 356
+++ +P+ G IIG+GG+TI LQ +GA I++ + P G+ ER+ + G +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP---GTTERVCLIQGTIEA 64
Query: 357 IEIAQEMIKE 366
+ I E
Sbjct: 65 LNAVHGFIAE 74
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 69.3 bits (168), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 53/172 (30%), Positives = 91/172 (52%), Gaps = 15/172 (8%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
+I +P K G++IGK G+TI+ LQ +G K+ + +D + + +P+ IIG + +A
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIGDPYKVQQA 63
Query: 263 EKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
+++ ++ E D GG G S +++ VP VG++IGR GE IK +Q
Sbjct: 64 CEMVMDILRERDQGGF------GDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQ 117
Query: 323 TRSGARIQVLIPQHLPEGDGSK-ERIVRVTGDMRQIEIAQEMIKEVLSQTVR 373
+G RIQ + DG+ E+I + G + E A +I ++L Q++R
Sbjct: 118 NDAGVRIQ------FKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL-QSLR 162
>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 = 59.3 bits (142), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 48/169 (28%), Positives = 82/169 (48%), Gaps = 13/169 (7%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
+P VG++IG+ G+ I+ +Q ++G +IQ D P R +I G A ++
Sbjct: 9 IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPE---RIAQITGPPDRAQHAAEI 65
Query: 266 INAVIAEADAGGSPSLVARGLATAQAS--------GAAEQVEIKVPNEKVGLIIGRGGET 317
I ++ AG G + G ++ VP K GLIIG+GGET
Sbjct: 66 ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGET 125
Query: 318 IKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKE 366
IK + +SGARI+ + ++ P ++ + G +QI+ A+++I+E
Sbjct: 126 IKSISQQSGARIE--LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEE 172
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDM 354
+ +++ +P VG++IGR GE IK +Q +G RI Q P+ + ERI ++TG
Sbjct: 2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRI-----QFKPDDGTTPERIAQITGPP 56
Query: 355 RQIEIAQEMIKEVL 368
+ + A E+I ++L
Sbjct: 57 DRAQHAAEIITDLL 70
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 40/67 (59%), Gaps = 4/67 (5%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD--ADADPHAATRPVEIIGTLSNIDKAE 263
VP K G++IGK G+TI+ + SGA+I++ R+ +ADP+ + I GT ID A
Sbjct: 110 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPN--MKLFTIRGTPQQIDYAR 167
Query: 264 KLINAVI 270
+LI I
Sbjct: 168 QLIEEKI 174
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
EI +P K GL+IG+GGETIK LQ R+G +++++ Q P+ G+ ++ +R+TGD +++
Sbjct: 18 EIMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGA-DKPLRITGDPYKVQ 74
Query: 359 IAQEMIKEVL 368
A+EM+ E++
Sbjct: 75 QAKEMVLELI 84
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 47/79 (59%), Gaps = 3/79 (3%)
Query: 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDK 261
++I +P +K G++IGK G+TI+ LQ +G K+ + +D + A +P+ I G + +
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQN-TGADKPLRITGDPYKVQQ 75
Query: 262 AEKLINAVIAEADAGGSPS 280
A++++ +I D G PS
Sbjct: 76 AKEMVLELI--RDQGSGPS 92
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 41/162 (25%), Positives = 78/162 (48%), Gaps = 32/162 (19%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
T++ ++ + +VG +IGK G++++ ++ SGA+I I+ + + R + + G +
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINIS-----EGNCPERIITLAGPTNA 58
Query: 259 --------IDKAEKLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLI 310
IDK E+ I++ + + A P + R + VP + G +
Sbjct: 59 IFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLR---------------LVVPASQCGSL 103
Query: 311 IGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTG 352
IG+GG IK ++ +GA++QV LP S ER + + G
Sbjct: 104 IGKGGCKIKEIRESTGAQVQV-AGDMLPN---STERAITIAG 141
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 10/86 (11%)
Query: 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364
++VG IIG+ GE++K ++ SGARI + EG+ ERI+ + G I A MI
Sbjct: 14 KEVGSIIGKKGESVKKMREESGARINI------SEGN-CPERIITLAGPTNAIFKAFAMI 66
Query: 365 KEVLSQTVRPSTLSGGFNQQAYRPRV 390
+ L + + S + + A RP V
Sbjct: 67 IDKLEEDISSSMTN---STAASRPPV 89
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
++ VP ++ G LIGK G I+ ++ ++GA++Q+ D P++ R + I G +I +
Sbjct: 92 RLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA--GDMLPNSTERAITIAGIPQSIIEC 149
Query: 263 EKLINAVIAE 272
K I V+ E
Sbjct: 150 VKQICVVMLE 159
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 49.7 bits (117), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
M+ + +VP+ VG +IG+ G+ I +Q SG KIQI D+ P R + GT +
Sbjct: 14 VMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPE---RSCMLTGTPES 70
Query: 259 IDKAEKLINAVIAEADAG 276
+ A++L++ ++ + +G
Sbjct: 71 VQSAKRLLDQIVEKGRSG 88
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
E KVP+ VG IIGRGGE I +Q SG +IQ+ P+ G ER +TG ++
Sbjct: 18 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQI-----APDSGGLPERSCMLTGTPESVQ 72
Query: 359 IAQEMIKEVL 368
A+ ++ +++
Sbjct: 73 SAKRLLDQIV 82
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
+M+ + VP+ VG++IG+ G+ I +Q +SG K+QI+ D+ P R V + G +
Sbjct: 15 SMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE---RSVSLTGAPES 71
Query: 259 IDKAEKLINAVIAEADAG 276
+ KA+ +++ +++ G
Sbjct: 72 VQKAKMMLDDIVSRGRGG 89
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
E +VP+ VGLIIGRGGE I +Q SG ++Q+ P+ G ER V +TG ++
Sbjct: 19 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQI-----SPDSGGLPERSVSLTGAPESVQ 73
Query: 359 IAQEMIKEVLSQ 370
A+ M+ +++S+
Sbjct: 74 KAKMMLDDIVSR 85
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 49/76 (64%), Gaps = 11/76 (14%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSK----ERIVRVTGDM 354
EI +P K GL+IG+GGETIK LQ R+G ++ +LI DGS+ ++ +R+ GD
Sbjct: 17 EIMIPAGKAGLVIGKGGETIKQLQERAGVKM-ILIQ------DGSQNTNVDKPLRIIGDP 69
Query: 355 RQIEIAQEMIKEVLSQ 370
+++ A EM+ ++L +
Sbjct: 70 YKVQQACEMVMDILRE 85
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 202 RKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDK 261
++I +P K G++IGK G+TI+ LQ +G K+ + +D + + +P+ IIG + +
Sbjct: 16 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTN-VDKPLRIIGDPYKVQQ 74
Query: 262 AEKLINAVIAE 272
A +++ ++ E
Sbjct: 75 ACEMVMDILRE 85
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
++ VP VG IIGRGGETI+ + SGA+I EG R+++++G +++
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITC---DKESEGTLLLSRLIKISGTQKEVA 74
Query: 359 IAQEMIKEVLSQ 370
A+ +I E +S+
Sbjct: 75 AAKHLILEKVSE 86
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
++ VP VG +IG+ G+TIR + SGAKI ++++ +R ++I GT + A
Sbjct: 18 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGT-LLLSRLIKISGTQKEVAAA 76
Query: 263 EKLINAVIAE 272
+ LI ++E
Sbjct: 77 KHLILEKVSE 86
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 47/167 (28%), Positives = 77/167 (46%), Gaps = 19/167 (11%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
+P VG +IGK G I+ L + A I+I P + R V I G KA+
Sbjct: 9 IPAQAVGAIIGKKGQHIKQLSRFASASIKIA--PPETPDSKVRMVIITGPPEAQFKAQGR 66
Query: 266 INAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRS 325
I + E + G V + I+VP G +IG+GG+T+ LQ +
Sbjct: 67 IYGKLKEENFFGPKEEVKL------------ETHIRVPASAAGRVIGKGGKTVNELQNLT 114
Query: 326 GARIQVLIPQ-HLPEGDGSKERIVRVTGDMRQIEIAQEMIKEVLSQT 371
A +V++P+ P D + + IV++ G ++AQ I+++L+Q
Sbjct: 115 AA--EVVVPRDQTP--DENDQVIVKIIGHFYASQMAQRKIRDILAQV 157
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 297 QVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQ 356
++ +P K GL+IGRGGE +K + ++GA ++ I + LP ++ + G +Q
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVE--ISRQLPPNGDPNFKLFIIRGSPQQ 65
Query: 357 IEIAQEMIKE 366
I+ A+++I+E
Sbjct: 66 IDHAKQLIEE 75
Score = 36.2 bits (82), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDA--DADPHAATRPVEIIGTLSNIDKAE 263
+P +K G++IG+ G+ ++ + +GA ++I+R + DP+ + G+ ID A+
Sbjct: 13 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIR--GSPQQIDHAK 70
Query: 264 KLINAVI 270
+LI I
Sbjct: 71 QLIEEKI 77
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
E+ +PN+ +G IIGR G I ++ SGA+I++ P +GS +R V +TG I
Sbjct: 8 ELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPV-----EGSTDRQVTITGSAASIS 62
Query: 359 IAQEMIKEVLS 369
+AQ +I LS
Sbjct: 63 LAQYLINVRLS 73
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
T S ++ +PN+ +G +IG+ G I ++ SGA+I+I A+ + R V I G+ ++
Sbjct: 4 TTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI---ANPVEGSTDRQVTITGSAAS 60
Query: 259 IDKAEKLINA 268
I A+ LIN
Sbjct: 61 ISLAQYLINV 70
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
E+ +PN +G IIGR G I ++ SGA+I++ P +GS R V +TG I
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPV-----EGSSGRQVTITGSAASIS 63
Query: 359 IAQEMIKEVLS 369
+AQ +I LS
Sbjct: 64 LAQYLINARLS 74
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
++ +PNN +G +IG+ G I ++ SGA+I+I A+ ++ R V I G+ ++I A
Sbjct: 9 ELTIPNNLIGCIIGRQGANINEIRQMSGAQIKI---ANPVEGSSGRQVTITGSAASISLA 65
Query: 263 EKLINA 268
+ LINA
Sbjct: 66 QYLINA 71
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 5/72 (6%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
++ +P + G IIG+GG+ IK ++ SGA I++ P +GS++RI+ +TG QI+
Sbjct: 17 QVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQ 71
Query: 359 IAQEMIKEVLSQ 370
AQ +++ + Q
Sbjct: 72 NAQYLLQNSVKQ 83
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
++ ++ +P + G +IGK G I+ +++ SGA I+I + + R + I GT
Sbjct: 13 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDRIITITGTQDQ 69
Query: 259 IDKAEKLI-NAV 269
I A+ L+ N+V
Sbjct: 70 IQNAQYLLQNSV 81
>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 = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 25/170 (14%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAE 263
+++P +++ VLIGK G T + ++ + K +IT D++ T E L+ + KA
Sbjct: 38 VKIPKDRIAVLIGKKGQTKKEIEKRT--KTKITIDSETGEVWITSTKETEDPLA-VWKAR 94
Query: 264 KLINAVIAEADAGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGL------IIGRGGET 317
++ A+ G SP R L + +I + NEK L IIGR G T
Sbjct: 95 DIVLAI----GRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRT 150
Query: 318 IKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMIKEV 367
+ ++ SGA + V + V + G+ QIEIA+ I+++
Sbjct: 151 RQIIEEMSGASVSVY------------GKTVAIIGNPIQIEIAKTAIEKL 188
>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 = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%), Gaps = 5/80 (6%)
Query: 291 ASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRV 350
A G ++ +P + G IIG+GG+ IK ++ SGA I++ P +GS++RI+ +
Sbjct: 2 AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITI 56
Query: 351 TGDMRQIEIAQEMIKEVLSQ 370
TG QI+ AQ +++ + Q
Sbjct: 57 TGTQDQIQNAQYLLQNSVKQ 76
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
++ ++ +P + G +IGK G I+ +++ SGA I+I + + R + I GT
Sbjct: 6 IITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDRIITITGTQDQ 62
Query: 259 IDKAEKLI 266
I A+ L+
Sbjct: 63 IQNAQYLL 70
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 36/68 (52%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
+I VP N VG ++GK G T+ Q +G +IQI++ + P R V I GT + A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 263 EKLINAVI 270
+ LI I
Sbjct: 66 QYLITQRI 73
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIP-QHLPEGDGSKERIVRVTGDMRQ 356
VEI VP VG I+G+GG+T+ Q +G RIQ+ + LP G++ R V +TG
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLP---GTRNRKVTITGTPAA 61
Query: 357 IEIAQEMIKE 366
+ AQ +I +
Sbjct: 62 TQAAQYLITQ 71
>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 = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 7/71 (9%)
Query: 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364
++VG IIG+ GE++K ++ SGARI + EG+ S ERI+ +TG I A MI
Sbjct: 12 KEVGSIIGKKGESVKRIREESGARINI------SEGN-SPERIITLTGPTNAIFKAFAMI 64
Query: 365 KEVLSQTVRPS 375
+ L + + S
Sbjct: 65 IDKLEEDINSS 75
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266
+VG +IGK G++++ ++ SGA+I I+ + ++ R + + G + I KA +I
Sbjct: 13 EVGSIIGKKGESVKRIREESGARINIS-----EGNSPERIITLTGPTNAIFKAFAMI 64
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 48/83 (57%), Gaps = 6/83 (7%)
Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIP-QHLPEGDGSKERIVRVTGDM 354
E VEI VP VG I+G+GG+T+ Q +GARIQ+ + LP G++ R V +TG
Sbjct: 3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGSP 59
Query: 355 RQIEIAQEMIKEVLS--QTVRPS 375
+ AQ +I + ++ Q VR S
Sbjct: 60 AATQAAQYLISQRVTYEQGVRAS 82
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 203 KIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKA 262
+I VP N VG ++GK G T+ Q +GA+IQI++ + P R V I G+ + A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAA 65
Query: 263 EKLIN 267
+ LI+
Sbjct: 66 QYLIS 70
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSK-E 345
A A S +++ VP VG++IGR GE IK +Q +G RIQ + DG+ E
Sbjct: 2 AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQ------FKQDDGTGPE 55
Query: 346 RIVRVTGDMRQIEIAQEMIKEVLSQTVR 373
+I + G + E A +I ++L Q++R
Sbjct: 56 KIAHIMGPPDRCEHAARIINDLL-QSLR 82
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 3/65 (4%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
VP + VGV+IG++G+ I+ +Q ++G +IQ +D P + I+G + A ++
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAARI 73
Query: 266 INAVI 270
IN ++
Sbjct: 74 INDLL 78
>pdb|4B8T|A Chain A, Rna Binding Protein Solution Structure Of The Third Kh
Domain Of Ksrp In Complex With The G-rich Target
Sequence
Length = 106
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 287 ATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSK-E 345
A A S +++ VP VG++IGR GE IK +Q +G RIQ + DG+ E
Sbjct: 2 AMAYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQ------FKQDDGTGPE 55
Query: 346 RIVRVTGDMRQIEIAQEMIKEVLSQTVR 373
+I + G + E A +I ++L Q++R
Sbjct: 56 KIAHIMGPPDRCEHAARIINDLL-QSLR 82
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 3/65 (4%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
VP + VGV+IG++G+ I+ +Q ++G +IQ +D P + I+G + A ++
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE---KIAHIMGPPDRCEHAARI 73
Query: 266 INAVI 270
IN ++
Sbjct: 74 INDLL 78
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 299 EIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIE 358
++ +P + IIG+GG+ IK ++ SGA I++ P +GS++RI+ +TG QI+
Sbjct: 17 QVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPL-----EGSEDRIITITGTQDQIQ 71
Query: 359 IAQEMIKEVLSQ 370
AQ +++ + Q
Sbjct: 72 NAQYLLQNSVKQ 83
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSN 258
++ ++ +P + +IGK G I+ +++ SGA I+I + + R + I GT
Sbjct: 13 IITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDRIITITGTQDQ 69
Query: 259 IDKAEKLI 266
I A+ L+
Sbjct: 70 IQNAQYLL 77
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 206 VPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKL 265
VP N VG ++GK G T+ Q +GA+IQI++ + P R V I G+ + A+ L
Sbjct: 9 VPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYL 68
Query: 266 IN 267
I+
Sbjct: 69 IS 70
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 296 EQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQVLIP-QHLPEGDGSKERIVRVTGD 353
E VE+ VP VG I+G+GG+T+ Q +GARIQ+ + LP G++ R V +TG
Sbjct: 3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP---GTRNRRVTITGS 58
>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 = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 7/68 (10%)
Query: 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQIEIAQEMI 364
++VG IIG+ GE++K ++ SGARI + EG+ ERI+ +TG I A MI
Sbjct: 12 KEVGSIIGKKGESVKRIREESGARINI------SEGN-CPERIITLTGPTNAIFKAFAMI 64
Query: 365 KEVLSQTV 372
+ L + +
Sbjct: 65 IDKLEEDI 72
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 210 KVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNIDKAEKLI 266
+VG +IGK G++++ ++ SGA+I I+ + + R + + G + I KA +I
Sbjct: 13 EVGSIIGKKGESVKRIREESGARINIS-----EGNCPERIITLTGPTNAIFKAFAMI 64
>pdb|2CTE|A Chain A, Solution Structure Of The 1st Kh Type I Domain From Human
Vigilin
Length = 94
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 201 SRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRDADADPHAATRPVEIIGTLSNID 260
S + +P +IGK G+ ++ L+ + KIQI R P + ++I GT I+
Sbjct: 18 SATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPR-----PDDPSNQIKITGTKEGIE 72
Query: 261 KAEKLINAVIAEADAGGSPS 280
KA + + AE D PS
Sbjct: 73 KARHEVLLISAEQDKRSGPS 92
Score = 29.3 bits (64), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 275 AGGSPSLVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQTRSGARIQV 331
+G S +VAR A A+ + +P E +IG+ GE ++ L+ ++ +IQ+
Sbjct: 3 SGSSGDIVARLQTQASAT-------VAIPKEHHRFVIGKNGEKLQDLELKTATKIQI 52
>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 = 33.9 bits (76), Expect = 0.39, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 305 EKVGLIIGRGGETIKGLQTRSGARIQVLIPQHLPEGDGSKERIVRVTGDMRQI 357
++VG IIG+ GE++K + SGARI + EG+ ERI+ + G I
Sbjct: 14 KEVGSIIGKKGESVKKXREESGARINI------SEGN-CPERIITLAGPTNAI 59
Score = 29.3 bits (64), Expect = 8.0, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 25/38 (65%)
Query: 199 TMSRKIEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQIT 236
T++ ++ +VG +IGK G++++ + SGA+I I+
Sbjct: 4 TLTIRLLXHGKEVGSIIGKKGESVKKXREESGARINIS 41
>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 = 33.5 bits (75), Expect = 0.49, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
L + GLA AA+ V + V K G++IGRGGE I+ L+
Sbjct: 46 LYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLR 87
>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 = 33.5 bits (75), Expect = 0.51, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 281 LVARGLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
L + GLA AA+ V + V K G++IGRGGE I+ L+
Sbjct: 46 LYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLR 87
>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 = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 285 GLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
GLA AA+ V + V K G++IGRGGE I+ L+
Sbjct: 50 GLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLR 87
>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 = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 285 GLATAQASGAAEQVEIKVPNEKVGLIIGRGGETIKGLQ 322
GLA AA+ V + V K G++IGRGGE I+ L+
Sbjct: 51 GLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLR 88
>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 = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238
I +P +K+ +IG G IR + +GAK+ I D
Sbjct: 565 INIPTDKIREVIGSGGKVIREIVATTGAKVDINDD 599
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238
I +P +K+ +IG G IR + +GAK+ I D
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDINDD 608
>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 = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSGAKIQITRD 238
I +P +K+ +IG G IR + +GAK+ I D
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDINDD 608
>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 = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 204 IEVPNNKVGVLIGKAGDTIRYLQYNSG---AKIQITRDADADPHAATRPVEIIGTLSNID 260
I+VP N VG +IGK G I+ + SG +I+ + + P +GT +I
Sbjct: 71 IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGXVPFVFVGTKDSIA 130
Query: 261 KAEKLIN 267
A L++
Sbjct: 131 NATVLLD 137
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 4/51 (7%)
Query: 295 AEQVEIKVPNEKVGLIIGRGGETIKGLQTRSG---ARIQVLIPQHLPEGDG 342
AE V I+VP VG +IG+ G+ I+ + +SG RI+ +++P+ +G
Sbjct: 67 AEDV-IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEG 116
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 29.3 bits (64), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 298 VEIKVPNEKVGLIIGRGGETIKGLQTRS 325
++++VP VGL++G G TIK +Q R+
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRT 39
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.308 0.128 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,685,793
Number of Sequences: 62578
Number of extensions: 892134
Number of successful extensions: 1405
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1290
Number of HSP's gapped (non-prelim): 95
length of query: 785
length of database: 14,973,337
effective HSP length: 107
effective length of query: 678
effective length of database: 8,277,491
effective search space: 5612138898
effective search space used: 5612138898
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)