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= 005922
(669 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 58/170 (34%), Positives = 90/170 (52%), Gaps = 16/170 (9%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
IP VG++IG++GE IK +Q +G +IQ D D +P R ++ G P++ A ++
Sbjct: 9 IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPD---DGTTPERIAQITGPPDRAQHAAEI 65
Query: 195 INDVLAEAESGGSGIVARRLTGQA------------GSDHFAMKIPNNKVGLVIGKGGET 242
I D+L ++G G G+ G F +P K GL+IGKGGET
Sbjct: 66 ITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGET 125
Query: 243 IKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVI 292
IK++ ++GARI+ + + PP + I GT +QI+ A+QL+ E I
Sbjct: 126 IKSISQQSGARIE-LQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTST-ERTVQIDGT 277
GS + IP VG+VIG+ GE IK +Q G RIQ P D +T ER QI G
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQ-----FKPDDGTTPERIAQITGP 55
Query: 278 SEQIESAKQLVNEVI 292
++ + A +++ +++
Sbjct: 56 PDRAQHAAEIITDLL 70
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 78.2 bits (191), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 56/172 (32%), Positives = 94/172 (54%), Gaps = 13/172 (7%)
Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD--TEADLNSPTRSVELMGTP 185
GT ++I IP + G++IGK GETIK LQ ++G K+ + +D +++ P R ++G P
Sbjct: 1 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR---IIGDP 57
Query: 186 EQIAKAEQLINDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKN 245
++ +A +++ D+L E + GG G R G + +P + VG+VIG+ GE IK
Sbjct: 58 YKVQQACEMVMDILRERDQGGFG--DRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKK 115
Query: 246 MQARTGARIQVIPLHLPPGD-TSTERTVQIDGTSEQIESAKQLVNEVISENR 296
+Q G RIQ D T E+ I G ++ E A +++N+++ R
Sbjct: 116 IQNDAGVRIQ-----FKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 162
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 3/71 (4%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
+P VGV+IG+SGE IK +Q +G +IQ +D D P + +MG P++ A ++
Sbjct: 97 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGPPDRCEHAARI 153
Query: 195 INDVLAEAESG 205
IND+L SG
Sbjct: 154 INDLLQSLRSG 164
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 68.6 bits (166), Expect = 1e-11, Method: Composition-based stats.
Identities = 52/153 (33%), Positives = 78/153 (50%), Gaps = 20/153 (13%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
VG IIGK GE++K ++ +SGA+I ++ N P R + L G I KA +I D L
Sbjct: 16 VGSIIGKKGESVKKMREESGARINISEG-----NCPERIITLAGPTNAIFKAFAMIIDKL 70
Query: 200 AEAESGGSGIVARRLTGQAGSDH----FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQ 255
E ++ +T + + +P ++ G +IGKGG IK ++ TGA++Q
Sbjct: 71 EED-------ISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQ 123
Query: 256 VIPLHLPPGDTSTERTVQIDGTSEQ-IESAKQL 287
V LP STER + I G + IE KQ+
Sbjct: 124 VAGDMLP---NSTERAITIAGIPQSIIECVKQI 153
Score = 37.0 bits (84), Expect = 0.034, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
++ +P + G +IGK G IK ++ +GA++QV D NS R++ + G P+ I +
Sbjct: 92 RLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP--NSTERAITIAGIPQSIIEC 149
Query: 192 EQLINDVLAE 201
+ I V+ E
Sbjct: 150 VKQICVVMLE 159
Score = 37.0 bits (84), Expect = 0.034, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 12/88 (13%)
Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
+VG +IGK GE++K M+ +GARI + + P ER + + G + I A ++ +
Sbjct: 15 EVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGPTNAIFKAFAMIID 68
Query: 291 VISENRIRNPAMAGGYSQQGYQARPPTS 318
+ E+ ++ + +RPP +
Sbjct: 69 KLEED------ISSSMTNSTAASRPPVT 90
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 50/170 (29%), Positives = 86/170 (50%), Gaps = 8/170 (4%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
K+ IP+ G IIGK G+TI LQ ++GA I++++ + + R + GT E +
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 192 EQLINDVLAE-----AESGGSGIVARRLTGQ-AGSDHFAMKIPNNKVGLVIGKGGETIKN 245
I + + E A++ I+ + T ++ + +PN+ GL+IGKGG T+K
Sbjct: 69 HGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKA 128
Query: 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
+ ++GA +Q+ P G R V + G EQ A +L+ + I E+
Sbjct: 129 IMEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 50/170 (29%), Positives = 86/170 (50%), Gaps = 8/170 (4%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
K+ IP+ G IIGK G+TI LQ ++GA I++++ + + R + GT E +
Sbjct: 9 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAV 68
Query: 192 EQLINDVLAE-----AESGGSGIVARRLTGQ-AGSDHFAMKIPNNKVGLVIGKGGETIKN 245
I + + E A++ I+ + T ++ + +PN+ GL+IGKGG T+K
Sbjct: 69 HGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKA 128
Query: 246 MQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISEN 295
+ ++GA +Q+ P G R V + G EQ A +L+ + I E+
Sbjct: 129 IXEQSGAWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELIIQKIQED 176
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 8/73 (10%)
Query: 226 KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLH--LPPGDTSTERTVQIDGTSEQIES 283
K+P+ VG +IG+GGE I +Q +G +IQ+ P LP ER+ + GT E ++S
Sbjct: 20 KVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP------ERSCMLTGTPESVQS 73
Query: 284 AKQLVNEVISENR 296
AK+L+++++ + R
Sbjct: 74 AKRLLDQIVEKGR 86
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 3/72 (4%)
Query: 134 EIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQ 193
++P+ VG IIG+ GE I +Q +SG KIQ+ D+ P RS L GTPE + A++
Sbjct: 20 KVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG---LPERSCMLTGTPESVQSAKR 76
Query: 194 LINDVLAEAESG 205
L++ ++ + SG
Sbjct: 77 LLDQIVEKGRSG 88
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 3/72 (4%)
Query: 134 EIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQ 193
+P+ VG+IIG+ GE I +Q SG K+Q++ D+ P RSV L G PE + KA+
Sbjct: 21 RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG---LPERSVSLTGAPESVQKAKM 77
Query: 194 LINDVLAEAESG 205
+++D+++ G
Sbjct: 78 MLDDIVSRGRGG 89
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 45/73 (61%), Gaps = 8/73 (10%)
Query: 226 KIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLH--LPPGDTSTERTVQIDGTSEQIES 283
++P+ VGL+IG+GGE I +Q +G ++Q+ P LP ER+V + G E ++
Sbjct: 21 RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP------ERSVSLTGAPESVQK 74
Query: 284 AKQLVNEVISENR 296
AK ++++++S R
Sbjct: 75 AKMMLDDIVSRGR 87
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/67 (43%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQ 286
IP +K GLVIG+GGE +K + +TGA ++ I LPP + I G+ +QI+ AKQ
Sbjct: 13 IPTHKCGLVIGRGGENVKAINQQTGAFVE-ISRQLPPNGDPNFKLFIIRGSPQQIDHAKQ 71
Query: 287 LVNEVIS 293
L+ E I
Sbjct: 72 LIEEKIE 78
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%)
Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
G IP + G++IG+ GE +K + Q+GA ++++R + + + + G+P+Q
Sbjct: 6 GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQ 65
Query: 188 IAKAEQLIND 197
I A+QLI +
Sbjct: 66 IDHAKQLIEE 75
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 47/70 (67%), Gaps = 2/70 (2%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IP +K GLVIGKGGETIK +Q R G ++++ + P +T ++ ++I G +++ A
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAG--VKMVMIQDGPQNTGADKPLRITGDPYKVQQA 76
Query: 285 KQLVNEVISE 294
K++V E+I +
Sbjct: 77 KEMVLELIRD 86
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 49/79 (62%), Gaps = 9/79 (11%)
Query: 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRD----TEADLNSPTRSVELMGTPE 186
++I IP + G++IGK GETIK LQ ++G K+ + +D T AD P R + G P
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD--KPLR---ITGDPY 71
Query: 187 QIAKAEQLINDVLAEAESG 205
++ +A++++ +++ + SG
Sbjct: 72 KVQQAKEMVLELIRDQGSG 90
>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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
+P VGV+IG+SGE IK +Q +G +IQ +D D P + +MG P++ A ++
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGPPDRCEHAARI 73
Query: 195 INDVLAEAES 204
IND+L S
Sbjct: 74 INDLLQSLRS 83
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD-TSTERTVQIDGTSEQIESAK 285
+P + VG+VIG+ GE IK +Q G RIQ D T E+ I G ++ E A
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQ-----FKQDDGTGPEKIAHIMGPPDRCEHAA 71
Query: 286 QLVNEVISENR 296
+++N+++ R
Sbjct: 72 RIINDLLQSLR 82
>pdb|2HH3|A Chain A, Solution Structure Of The Third Kh Domain Of Ksrp
Length = 106
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
+P VGV+IG+SGE IK +Q +G +IQ +D D P + +MG P++ A ++
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMGPPDRCEHAARI 73
Query: 195 INDVLAEAES 204
IND+L S
Sbjct: 74 INDLLQSLRS 83
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 227 IPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGD-TSTERTVQIDGTSEQIESAK 285
+P + VG+VIG+ GE IK +Q G RIQ D T E+ I G ++ E A
Sbjct: 17 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQ-----FKQDDGTGPEKIAHIMGPPDRCEHAA 71
Query: 286 QLVNEVISENR 296
+++N+++ R
Sbjct: 72 RIINDLLQSLR 82
>pdb|2OPV|A Chain A, Solution Nmr Structure Of The Second Domain Of Ksrp
Length = 85
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 48/74 (64%), Gaps = 1/74 (1%)
Query: 128 GTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQ 187
GT ++I IP + G++IGK GETIK LQ ++G K+ + +D + N + + ++G P +
Sbjct: 13 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIGDPYK 71
Query: 188 IAKAEQLINDVLAE 201
+ +A +++ D+L E
Sbjct: 72 VQQACEMVMDILRE 85
Score = 45.8 bits (107), Expect = 7e-05, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 49/79 (62%), Gaps = 3/79 (3%)
Query: 216 GQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQID 275
GQ G+ M IP K GLVIGKGGETIK +Q R G +++I + +T+ ++ ++I
Sbjct: 10 GQNGTVQEIM-IPAGKAGLVIGKGGETIKQLQERAG--VKMILIQDGSQNTNVDKPLRII 66
Query: 276 GTSEQIESAKQLVNEVISE 294
G +++ A ++V +++ E
Sbjct: 67 GDPYKVQQACEMVMDILRE 85
>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 = 45.8 bits (107), Expect = 7e-05, Method: Composition-based stats.
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
VG IIGK GE++K ++ +SGA+I ++ NSP R + L G I KA +I D L
Sbjct: 14 VGSIIGKKGESVKRIREESGARINISEG-----NSPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 200 AE 201
E
Sbjct: 69 EE 70
Score = 35.4 bits (80), Expect = 0.092, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
+VG +IGK GE++K ++ +GARI + S ER + + G + I A ++ +
Sbjct: 13 EVGSIIGKKGESVKRIREESGARINI------SEGNSPERIITLTGPTNAIFKAFAMIID 66
Query: 291 VISEN 295
+ E+
Sbjct: 67 KLEED 71
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
VG IIGK GE++K ++ +SGA+I ++ N P R + L G I KA +I D L
Sbjct: 14 VGSIIGKKGESVKRIREESGARINISEG-----NCPERIITLTGPTNAIFKAFAMIIDKL 68
Query: 200 AE 201
E
Sbjct: 69 EE 70
Score = 36.2 bits (82), Expect = 0.068, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
+VG +IGK GE++K ++ +GARI + + P ER + + G + I A ++ +
Sbjct: 13 EVGSIIGKKGESVKRIREESGARINISEGNCP------ERIITLTGPTNAIFKAFAMIID 66
Query: 291 VISEN 295
+ E+
Sbjct: 67 KLEED 71
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 131 KKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAK 190
+++ +P VG IIG+ GETI+ + SGAKI +++E L +R +++ GT +++A
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL-LLSRLIKISGTQKEVAA 75
Query: 191 AEQLINDVLAEAE 203
A+ LI + ++E E
Sbjct: 76 AKHLILEKVSEDE 88
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ +P VG +IG+GGETI+++ +GA+I G R ++I GT +++ +A
Sbjct: 19 LSVPQRSVGRIIGRGGETIRSICKASGAKITCD--KESEGTLLLSRLIKISGTQKEVAAA 76
Query: 285 KQLVNEVISEN 295
K L+ E +SE+
Sbjct: 77 KHLILEKVSED 87
>pdb|2CTE|A Chain A, Solution Structure Of The 1st Kh Type I Domain From Human
Vigilin
Length = 94
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 34/96 (35%), Positives = 51/96 (53%), Gaps = 9/96 (9%)
Query: 204 SGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPP 263
SG SG + RL QA + + IP VIGK GE +++++ +T +IQ IP P
Sbjct: 3 SGSSGDIVARLQTQASA---TVAIPKEHHRFVIGKNGEKLQDLELKTATKIQ-IP---RP 55
Query: 264 GDTSTERTVQIDGTSEQIESAKQLVNEVISENRIRN 299
D S + ++I GT E IE A+ V + +E R+
Sbjct: 56 DDPSNQ--IKITGTKEGIEKARHEVLLISAEQDKRS 89
Score = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
+ IP +IGK+GE ++ L+L++ KIQ+ R + P+ +++ GT E I KA
Sbjct: 21 VAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRP-----DDPSNQIKITGTKEGIEKAR 75
Query: 193 QLINDVLAE 201
+ + AE
Sbjct: 76 HEVLLISAE 84
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IP + G +IGKGG+ IK ++ +GA I++ P + S +R + I GT +QI++A
Sbjct: 18 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSEDRIITITGTQDQIQNA 73
Query: 285 KQLV 288
+ L+
Sbjct: 74 QYLL 77
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 119 VSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRS 178
+SYG + ++ IP G IIGK G+ IK ++ +SGA I++ E S R
Sbjct: 4 MSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDRI 60
Query: 179 VELMGTPEQIAKAEQLIND 197
+ + GT +QI A+ L+ +
Sbjct: 61 ITITGTQDQIQNAQYLLQN 79
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 140 VGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVL 199
VG IIGK GE++K + +SGA+I ++ N P R + L G I KA I D L
Sbjct: 16 VGSIIGKKGESVKKXREESGARINISEG-----NCPERIITLAGPTNAIFKAFAXIIDKL 70
Query: 200 AE 201
E
Sbjct: 71 EE 72
Score = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 231 KVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNE 290
+VG +IGK GE++K + +GARI + + P ER + + G + I A + +
Sbjct: 15 EVGSIIGKKGESVKKXREESGARINISEGNCP------ERIITLAGPTNAIFKAFAXIID 68
Query: 291 VISEN 295
+ E+
Sbjct: 69 KLEED 73
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IP + G +IGKGG+ IK ++ +GA I++ P + S +R + I GT +QI++A
Sbjct: 11 VTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGSEDRIITITGTQDQIQNA 66
Query: 285 KQLV 288
+ L+
Sbjct: 67 QYLL 70
Score = 36.2 bits (82), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
+ ++ IP G IIGK G+ IK ++ +SGA I++ E S R + + GT +QI
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDRIITITGTQDQI 63
Query: 189 AKAEQLIND 197
A+ L+ +
Sbjct: 64 QNAQYLLQN 72
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 77/162 (47%), Gaps = 12/162 (7%)
Query: 135 IPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQL 194
IP VG IIGK G+ IK L + A I++ D S R V + G PE KA+
Sbjct: 9 IPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPD--SKVRMVIITGPPEAQFKAQGR 66
Query: 195 INDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI 254
I L E G + T +++P + G VIGKGG+T+ +Q T A +
Sbjct: 67 IYGKLKEENFFGPKEEVKLETH--------IRVPASAAGRVIGKGGKTVNELQNLTAAEV 118
Query: 255 QVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEVISENR 296
V+P P D + + V+I G + A++ + +++++ +
Sbjct: 119 -VVPRDQTP-DENDQVIVKIIGHFYASQMAQRKIRDILAQVK 158
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 121 YGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVE 180
+G + + I +P G +IGK G+T+ LQ + A++ V RD D N V+
Sbjct: 77 FGPKEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQV-IVK 135
Query: 181 LMGTPEQIAKAEQLINDVLAEAE 203
++G A++ I D+LA+ +
Sbjct: 136 IIGHFYASQMAQRKIRDILAQVK 158
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IPNN +G +IG+ G I ++ +GA+I++ P + S+ R V I G++ I A
Sbjct: 10 LTIPNNLIGCIIGRQGANINEIRQMSGAQIKI----ANPVEGSSGRQVTITGSAASISLA 65
Query: 285 KQLVNEVISENR 296
+ L+N +S +
Sbjct: 66 QYLINARLSSEK 77
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
T+ ++ IPN +G IIG+ G I ++ SGA+I++ E S R V + G+ I
Sbjct: 6 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEG---SSGRQVTITGSAASI 62
Query: 189 AKAEQLINDVLAEAESGGS 207
+ A+ LIN L+ + G
Sbjct: 63 SLAQYLINARLSSEKGMGC 81
>pdb|1DT4|A Chain A, Crystal Structure Of Nova-1 Kh3 K-Homology Rna-Binding
Domain
Length = 73
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL-HLPPGDTSTERTVQIDGTSE 279
D + +P N VG ++GKGG+T+ Q TG RIQ+ PG + R V I GT
Sbjct: 3 DVVEIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPG--TRNRKVTITGTPA 60
Query: 280 QIESAKQLVNEVI 292
++A+ L+ + I
Sbjct: 61 ATQAAQYLITQRI 73
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 132 KIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKA 191
+I +P VG I+GK G+T+ Q +G +IQ+++ E + R V + GTP A
Sbjct: 6 EIAVPENLVGAILGKGGKTLVEYQELTGCRIQISKKGEFLPGTRNRKVTITGTPAATQAA 65
Query: 192 EQLI 195
+ LI
Sbjct: 66 QYLI 69
>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 = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+ M +P N VG ++GKGG+T+ Q TGARIQ+
Sbjct: 3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQI 38
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%)
Query: 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPE 186
M ++ +P VG I+GK G+T+ Q +GA+IQ+++ E + R V + G+P
Sbjct: 1 MKELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60
Query: 187 QIAKAEQLIN 196
A+ LI+
Sbjct: 61 ATQAAQYLIS 70
>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 = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IPN+ +G +IG+ G I ++ +GA+I++ P + ST+R V I G++ I A
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKI----ANPVEGSTDRQVTITGSAASISLA 64
Query: 285 KQLVN 289
+ L+N
Sbjct: 65 QYLIN 69
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 129 TSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQI 188
TS ++ IPN +G IIG+ G I ++ SGA+I++ E S R V + G+ I
Sbjct: 5 TSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEG---STDRQVTITGSAASI 61
Query: 189 AKAEQLIN 196
+ A+ LIN
Sbjct: 62 SLAQYLIN 69
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 4/64 (6%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESA 284
+ IP + +IGKGG+ IK ++ +GA I++ P + S +R + I GT +QI++A
Sbjct: 18 VTIPKDLARSIIGKGGQRIKQIRHESGASIKI----DEPLEGSEDRIITITGTQDQIQNA 73
Query: 285 KQLV 288
+ L+
Sbjct: 74 QYLL 77
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 118 PVSYGGYQSMGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTR 177
P SYG + ++ IP IIGK G+ IK ++ +SGA I++ E S R
Sbjct: 3 PNSYGDLGGPIITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKIDEPLEG---SEDR 59
Query: 178 SVELMGTPEQIAKAEQLIND 197
+ + GT +QI A+ L+ +
Sbjct: 60 IITITGTQDQIQNAQYLLQN 79
>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 = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 44/172 (25%), Positives = 76/172 (44%), Gaps = 34/172 (19%)
Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAE 192
++IP R+ V+IGK G+T K ++ ++ KI + +T + T+ E P + KA
Sbjct: 38 VKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETE---DPLAVWKAR 94
Query: 193 QLINDVLAEAESGGSGIVARRLTGQA-------------GSDHFAMKIPNNKVGLVIGKG 239
D++ G S A RL + G++ A+ P + G +IG+
Sbjct: 95 ----DIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNAL--PRVR-GRIIGRK 147
Query: 240 GETIKNMQARTGARIQVIPLHLPPGDTSTERTVQIDGTSEQIESAKQLVNEV 291
G T + ++ +GA + V +TV I G QIE AK + ++
Sbjct: 148 GRTRQIIEEMSGASVSVY-----------GKTVAIIGNPIQIEIAKTAIEKL 188
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 221 DHFAMKIPNNKVGLVIGKGGETIKNMQARTGARIQVIPL-HLPPGDTSTERTVQIDGTSE 279
+ + +P N VG ++GKGG+T+ Q TGARIQ+ PG + R V I G+
Sbjct: 3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPG--TRNRRVTITGSPA 60
Query: 280 QIESAKQLVNEVIS 293
++A+ L+++ ++
Sbjct: 61 ATQAAQYLISQRVT 74
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%)
Query: 127 MGTSKKIEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRSVELMGTPE 186
M +I +P VG I+GK G+T+ Q +GA+IQ+++ E + R V + G+P
Sbjct: 1 MKELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPA 60
Query: 187 QIAKAEQLIN 196
A+ LI+
Sbjct: 61 ATQAAQYLIS 70
>pdb|3IZ6|AA Chain a, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 380
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%)
Query: 195 INDVLAEAESGGSGIVARRLTGQAGSDHFAMKIPNNKVGLVIGKGGETIKNMQARTGARI 254
I ++ ++A+ G+ V+R LTG G +P+ + L+ G G +T TG RI
Sbjct: 134 IFNLSSQADRDGNMPVSRVLTGHKGYASSCQYVPDQETRLITGSGDQTCVLWDVTTGQRI 193
Query: 255 QVIPLHLPPGDTSTERTVQID 275
+ P G T+ ++ I+
Sbjct: 194 SIFGSEFPSGHTADVLSLSIN 214
>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 = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+ IP +K+ VIG GG+ I+ + A TGA++ +
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDI 605
>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 = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+ IP +K+ VIG GG+ I+ + A TGA++ +
Sbjct: 565 INIPTDKIREVIGSGGKVIREIVATTGAKVDI 596
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+ IP +K+ VIG GG+ I+ + A TGA++ +
Sbjct: 574 INIPTDKIREVIGSGGKVIREIVATTGAKVDI 605
>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 = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 133 IEIPNIRVGVIIGKSGETIKYLQLQSGAKIQVTRDTEADLNSPTRS----VELMGTPEQI 188
I++P VG +IGK+G+ I+ + +SG ++V + E + N P +GT + I
Sbjct: 71 IQVPRNLVGKVIGKNGKLIQEIVDKSGV-VRVRIEAENEKNVPQEEGXVPFVFVGTKDSI 129
Query: 189 AKAEQLIN 196
A A L++
Sbjct: 130 ANATVLLD 137
>pdb|2DGR|A Chain A, Solution Structure Of The Second Kh Domain In Ring Finger
And Kh Domain Containing Protein 1
Length = 83
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 225 MKIPNNKVGLVIGKGGETIKNMQART 250
+++P VGLV+G G TIK +Q RT
Sbjct: 14 VRVPYRVVGLVVGPKGATIKRIQQRT 39
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+KIP +K+G VIG + I +Q TGA I +
Sbjct: 600 ITVKIPVDKIGEVIGPKRQXINQIQEDTGAEITI 633
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 223 FAMKIPNNKVGLVIGKGGETIKNMQARTGARIQV 256
+KIP +K+G VIG + I +Q TGA I +
Sbjct: 600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITI 633
>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 = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 159 GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA 218
G ++ +TRD E+ + + + +Q + L E E +G+ R+ +
Sbjct: 8 GFRLGITRDWESRWYAGKKQYRHLLLEDQRIRG-------LLEKELYSAGLA--RVDIER 58
Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQ 247
+D+ A+ + K G+VIG+GGE I+ ++
Sbjct: 59 AADNVAVTVHVAKPGVVIGRGGERIRVLR 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 = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 159 GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA 218
G ++ +TRD E+ + + + +Q + L E E +G+ R+ +
Sbjct: 9 GFRLGITRDWESRWYAGKKQYRHLLLEDQRIRG-------LLEKELYSAGLA--RVDIER 59
Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQ 247
+D+ A+ + K G+VIG+GGE I+ ++
Sbjct: 60 AADNVAVTVHVAKPGVVIGRGGERIRVLR 88
>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 = 28.9 bits (63), Expect = 9.2, Method: Composition-based stats.
Identities = 41/176 (23%), Positives = 71/176 (40%), Gaps = 24/176 (13%)
Query: 159 GAKIQVTRDTEADLNSPTRSVELMGTPEQIAKAEQLINDVLAEAESGGSGIVARRLTGQA 218
G ++ +TRD E+ + + + +Q + L E E +G+ R+ +
Sbjct: 8 GFRLGITRDWESRWYAGKKQYRHLLLEDQRIRG-------LLEKELYSAGLA--RVDIER 58
Query: 219 GSDHFAMKIPNNKVGLVIGKGGETIKNMQAR----TGARIQVIPLHLPPGDTSTERTVQI 274
+D+ A+ + K G+VIG+GGE I+ ++ TG + + + + S Q
Sbjct: 59 AADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQ- 117
Query: 275 DGTSEQIE-------SAKQLVNEVISENRIRNPAMAGGYSQQGYQARPPTSWGTPG 323
+EQIE + KQ V V+ + G QAR T W G
Sbjct: 118 -RVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQAR--TEWAAQG 170
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
0.306 0.127 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,168,154
Number of Sequences: 62578
Number of extensions: 933587
Number of successful extensions: 1287
Number of sequences better than 100.0: 68
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 1151
Number of HSP's gapped (non-prelim): 131
length of query: 669
length of database: 14,973,337
effective HSP length: 105
effective length of query: 564
effective length of database: 8,402,647
effective search space: 4739092908
effective search space used: 4739092908
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 55 (25.8 bits)