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= 020173
(330 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JZX|A Chain A, Pcbp2 Kh1-Kh2 Domains
Length = 160
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 45/146 (30%), Positives = 73/146 (50%), Gaps = 25/146 (17%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
TIRLL+ G + G +IG G++++K+R SGA I I + + +R++ ++G
Sbjct: 6 TIRLLMHGKEVGSIIGKKGESVKKMREESGARINI---------SEGNCPERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
A+ A I ++L E+ IS S + +A RP VT +++ S
Sbjct: 57 NAIFKAFAMIIDKLEED-----ISSSMTNSTAASRPP-----------VTLRLVVPASQC 100
Query: 264 GGLIGRCGSNISRIRNESGAMIKVYG 289
G LIG+ G I IR +GA ++V G
Sbjct: 101 GSLIGKGGCKIKEIRESTGAQVQVAG 126
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 46/171 (26%), Positives = 88/171 (51%), Gaps = 21/171 (12%)
Query: 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDND 105
K + R+++ +++G +IGK+G ++K+REE ER+I ++ N
Sbjct: 1 KNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN- 57
Query: 106 NVVSDAENALQQIAALI---LKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSG 162
A+ + A+I L++D S+S + AA T+RL++ SQ G LIG G
Sbjct: 58 --------AIFKAFAMIIDKLEEDISSSMTNSTAASRPPV-TLRLVVPASQCGSLIGKGG 108
Query: 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213
I+++R S+GA + + A + LP + ++R + I+G +++ + +I
Sbjct: 109 CKIKEIRESTGAQVQV-AGDMLP-----NSTERAITIAGIPQSIIECVKQI 153
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV--- 308
+T +L+ VG +IG+ G ++ ++R ESGA I + +G R I G +
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINIS--EGNCPERIITLAGPTNAIFKA 62
Query: 309 -ALAKQRVDEYIYSQLIQQAGA 329
A+ +++E I S + A
Sbjct: 63 FAMIIDKLEEDISSSMTNSTAA 84
>pdb|2ANR|A Chain A, Crystal Structure (Ii) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25NT RNA Hairpin
Length = 178
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 44/144 (30%), Positives = 74/144 (51%), Gaps = 13/144 (9%)
Query: 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204
+++LI AG +IG GQ I +L+ +GATI + ++RV I G +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF----YPGTTERVCLIQGTIE 63
Query: 205 AVLNAL-VEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
A LNA+ I ++RE P+ V P S ++P Q V P A+ V ++++ S
Sbjct: 64 A-LNAVHGFIAEKIREX-PQNVAKTEPV---SILQP-QTTVNPDRANQV--KIIVPNSTA 115
Query: 264 GGLIGRCGSNISRIRNESGAMIKV 287
G +IG+ G+ + I +SGA +++
Sbjct: 116 GLIIGKGGATVKAIXEQSGAWVQL 139
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 41/182 (22%), Positives = 80/182 (43%), Gaps = 22/182 (12%)
Query: 51 LFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRH---EERVIIISSKDNDNV 107
++++PS G +IGK G I ++++E + ERV +I
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG------ 60
Query: 108 VSDAENALQQIAALILKDDDSN---SEASKVAAGHVA-----ANTIRLLIAGSQAGCLIG 159
+A NA+ A +++ N +E + AN +++++ S AG +IG
Sbjct: 61 TIEALNAVHGFIAEKIREXPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIG 120
Query: 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
G ++ + SGA + + +Q P + +RVV +SG+ A+ I +++E
Sbjct: 121 KGGATVKAIXEQSGAWVQL---SQKP--DGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175
Query: 220 NP 221
+P
Sbjct: 176 DP 177
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 246 PTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291
P + Y ++LI G +IG+ G I +++ E+GA IK+ K
Sbjct: 1 PLGSQYF-LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
>pdb|2ANN|A Chain A, Crystal Structure (I) Of Nova-1 Kh1KH2 DOMAIN TANDEM WITH
25 NT RNA Hairpin
Length = 178
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 44/144 (30%), Positives = 74/144 (51%), Gaps = 13/144 (9%)
Query: 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204
+++LI AG +IG GQ I +L+ +GATI + ++RV I G +
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF----YPGTTERVCLIQGTIE 63
Query: 205 AVLNAL-VEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLV 263
A LNA+ I ++RE P+ V P S ++P Q V P A+ V ++++ S
Sbjct: 64 A-LNAVHGFIAEKIREM-PQNVAKTEPV---SILQP-QTTVNPDRANQV--KIIVPNSTA 115
Query: 264 GGLIGRCGSNISRIRNESGAMIKV 287
G +IG+ G+ + I +SGA +++
Sbjct: 116 GLIIGKGGATVKAIMEQSGAWVQL 139
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 41/182 (22%), Positives = 80/182 (43%), Gaps = 22/182 (12%)
Query: 51 LFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRH---EERVIIISSKDNDNV 107
++++PS G +IGK G I ++++E + ERV +I
Sbjct: 7 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG------ 60
Query: 108 VSDAENALQQIAALILKDDDSN---SEASKVAAGHVA-----ANTIRLLIAGSQAGCLIG 159
+A NA+ A +++ N +E + AN +++++ S AG +IG
Sbjct: 61 TIEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIG 120
Query: 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219
G ++ + SGA + + +Q P + +RVV +SG+ A+ I +++E
Sbjct: 121 KGGATVKAIMEQSGAWVQL---SQKP--DGINLQNRVVTVSGEPEQNRKAVELIIQKIQE 175
Query: 220 NP 221
+P
Sbjct: 176 DP 177
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 246 PTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291
P + Y ++LI G +IG+ G I +++ E+GA IK+ K
Sbjct: 1 PLGSQYF-LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 45
>pdb|1WVN|A Chain A, Crsytal Structure Of Domain 3 Of Human Alpha Polyc Binding
Protein
Length = 82
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
T E+ I +L+G +IGR G+NI+ IR SGA IK+ R + GSA ++LA
Sbjct: 6 TTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLA 65
Query: 312 KQRVDEYIYSQ 322
+ ++ + S+
Sbjct: 66 QYLINARLSSE 76
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
T L I + GC+IG G NI ++R SGA I I P + S R V I+G
Sbjct: 7 THELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE-------GSSGRQVTITGSA 59
Query: 204 PAV 206
++
Sbjct: 60 ASI 62
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
TIRLL+ G + G +IG G++++++R SGA I I + + +R++ ++G
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINI---------SEGNSPERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
A+ A I ++L E+
Sbjct: 55 NAIFKAFAMIIDKLEED 71
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQK 295
+T +L+ VG +IG+ G ++ RIR ESGA I + G ++
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNSPER 46
Score = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 10/26 (38%), Positives = 21/26 (80%)
Query: 53 RIIVPSRQIGKVIGKEGHRIQKIREE 78
R+++ +++G +IGK+G +++IREE
Sbjct: 6 RLLMHGKEVGSIIGKKGESVKRIREE 31
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 249 ADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQV 308
A + E+ I L+G +IGR G+ I+ IR SGA IK+ R + GSA +
Sbjct: 2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVEGSTDRQVTITGSAASI 61
Query: 309 ALAKQRVDEYIYSQ 322
+LA+ ++ + S+
Sbjct: 62 SLAQYLINVRLSSE 75
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206
L I GC+IG G I ++R SGA I I P + +DR V I+G ++
Sbjct: 9 LTIPNDLIGCIIGRQGAKINEIRQXSGAQIKIANPVE-------GSTDRQVTITGSAASI 61
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIRE 77
KAQ + +P+ IG +IG++G +I +IR+
Sbjct: 1 KAQTTSHELTIPNDLIGCIIGRQGAKINEIRQ 32
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
TIRLL+ G + G +IG G++++++R SGA I I N C +R++ ++G
Sbjct: 4 TIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGN----CP-----ERIITLTGPT 54
Query: 204 PAVLNALVEIGNQLREN 220
A+ A I ++L E+
Sbjct: 55 NAIFKAFAMIIDKLEED 71
Score = 31.6 bits (70), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290
+T +L+ VG +IG+ G ++ RIR ESGA I + G
Sbjct: 3 LTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEG 41
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 21/27 (77%)
Query: 52 FRIIVPSRQIGKVIGKEGHRIQKIREE 78
R+++ +++G +IGK+G +++IREE
Sbjct: 5 IRLLMHGKEVGSIIGKKGESVKRIREE 31
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
TIRLL G + G +IG G++++K R SGA I I N C +R++ ++G
Sbjct: 6 TIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEGN----CP-----ERIITLAGPT 56
Query: 204 PAVLNALVEIGNQLREN 220
A+ A I ++L E+
Sbjct: 57 NAIFKAFAXIIDKLEED 73
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREE 78
+ R++ +++G +IGK+G ++K REE
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREE 33
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290
+T +L VG +IG+ G ++ + R ESGA I + G
Sbjct: 5 LTIRLLXHGKEVGSIIGKKGESVKKXREESGARINISEG 43
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%)
Query: 244 VEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG 303
+ P +T E + + +VG +IGR G I++I+ +SG +++ G R + G
Sbjct: 8 IHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTG 67
Query: 304 SAQQVALAKQRVDEYI 319
+ + V AK +D+ +
Sbjct: 68 APESVQKAKMMLDDIV 83
>pdb|1X4N|A Chain A, Solution Structure Of Kh Domain In Fuse Binding Protein 1
Length = 92
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 37/68 (54%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALA 311
+T E + + +VG +IGR G ISRI+ ESG I++ G R G+ + V A
Sbjct: 15 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSA 74
Query: 312 KQRVDEYI 319
K+ +D+ +
Sbjct: 75 KRLLDQIV 82
>pdb|1J5K|A Chain A, Complex Of The Kh3 Domain Of Hnrnp K With A
Single_stranded 10mer Dna Oligonucleotide
Length = 89
Score = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
T ++ I AG +IG GQ I+++R+ SGA+I I PL S DR++ I+G
Sbjct: 15 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGS---EDRIITITGTQ 67
Query: 204 PAVLNALVEIGNQLRE 219
+ NA + N +++
Sbjct: 68 DQIQNAQYLLQNSVKQ 83
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287
+T ++ I + L G +IG+ G I +IR+ESGA IK+
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI 49
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVS 109
+ ++ +P G +IGK G RI++IR E E+R+I I+ + +
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ--IQ 71
Query: 110 DAENALQ 116
+A+ LQ
Sbjct: 72 NAQYLLQ 78
>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 = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
T ++ I AG +IG GQ I+++R+ SGA+I I PL S DR++ I+G
Sbjct: 8 TTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI----DEPLEGS---EDRIITITGTQ 60
Query: 204 PAVLNALVEIGNQLRE 219
+ NA + N +++
Sbjct: 61 DQIQNAQYLLQNSVKQ 76
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 25/36 (69%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287
+T ++ I + L G +IG+ G I +IR+ESGA IK+
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI 42
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNVVS 109
+ ++ +P G +IGK G RI++IR E E+R+I I+ + +
Sbjct: 7 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQ--IQ 64
Query: 110 DAENALQ 116
+A+ LQ
Sbjct: 65 NAQYLLQ 71
>pdb|3KRM|A Chain A, Imp1 Kh34
pdb|3KRM|B Chain B, Imp1 Kh34
pdb|3KRM|C Chain C, Imp1 Kh34
Length = 163
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 33/143 (23%), Positives = 59/143 (41%), Gaps = 27/143 (18%)
Query: 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204
+++ I G +IG GQ+I++L + A+I I AP + P R+V I+G
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKI-APPETP-----DSKVRMVIITGPPE 58
Query: 205 AVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVG 264
A A I +L+E + F P + + + S G
Sbjct: 59 AQFKAQGRIYGKLKE---------------------ENFFGPKEEVKLETHIRVPASAAG 97
Query: 265 GLIGRCGSNISRIRNESGAMIKV 287
+IG+ G ++ ++N + A + V
Sbjct: 98 RVIGKGGKTVNELQNLTAAEVVV 120
>pdb|1KHM|A Chain A, C-Terminal Kh Domain Of Hnrnp K (Kh3)
Length = 89
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203
T ++ I A +IG GQ I+++R+ SGA+I I PL S DR++ I+G
Sbjct: 15 TTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI----DEPLEGS---EDRIITITGTQ 67
Query: 204 PAVLNALVEIGNQLRE 219
+ NA + N +++
Sbjct: 68 DQIQNAQYLLQNSVKQ 83
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287
+T ++ I + L +IG+ G I +IR+ESGA IK+
Sbjct: 14 ITTQVTIPKDLARSIIGKGGQRIKQIRHESGASIKI 49
>pdb|2JVZ|A Chain A, Solution Nmr Structure Of The Second And Third Kh Domains
Of Ksrp
Length = 164
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 31/131 (23%), Positives = 56/131 (42%), Gaps = 20/131 (15%)
Query: 54 IIVPSRQIGKVIGKEGHRIQKIREEXXXXXXXXXXXXRHEERVIIISSKDNDNV------ 107
I++P+ + G VIGK G I++++E + ++I N NV
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAGV------------KMILIQDGSQNTNVDKPLRI 53
Query: 108 VSDAENALQ--QIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNI 165
+ D Q ++ IL++ D + G I + + G +IG SG+ I
Sbjct: 54 IGDPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMI 113
Query: 166 EKLRNSSGATI 176
+K++N +G I
Sbjct: 114 KKIQNDAGVRI 124
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 37/155 (23%), Positives = 66/155 (42%), Gaps = 22/155 (14%)
Query: 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206
++I +AG +IG G+ I++L+ +G ++++ + D+ ++I GD V
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-----SQNTNVDKPLRIIGDPYKV 60
Query: 207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGL 266
A + + LRE R Y S ++ + VG +
Sbjct: 61 QQACEMVMDILRE---RDQGGFGDRNEYG------------SRIGGGIDVPVPRHSVGVV 105
Query: 267 IGRCGSNISRIRNESGAMIKVY--GGKGEQKHRHI 299
IGR G I +I+N++G I+ G G +K HI
Sbjct: 106 IGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHI 140
>pdb|2HH2|A Chain A, Solution Structure Of The Fourth Kh Domain Of Ksrp
Length = 107
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV---YGGKGEQKHRHIQFGGSAQQV 308
+TF I G +IGR G N+ I ++GA +++ G+ + GS QQ+
Sbjct: 9 MTFS--IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQI 66
Query: 309 ALAKQRVDEYI 319
AKQ ++E I
Sbjct: 67 DHAKQLIEEKI 77
>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 = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG---KGEQKHRHIQFGGSAQQVAL 310
F ++ G +IG+ G I I +SGA I++ + + G+ QQ+
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 165
Query: 311 AKQRVDEYI 319
A+Q ++E I
Sbjct: 166 ARQLIEEKI 174
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQR 314
++ I VG +IGR G I +I+N++G I+ G R Q G + A +
Sbjct: 6 DVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEI 65
Query: 315 VDEYIYS 321
+ + + S
Sbjct: 66 ITDLLRS 72
>pdb|1P6G|C Chain C, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P87|C Chain C, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AVY|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AW7|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|2I2P|C Chain C, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2U|C Chain C, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QOU|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The First 70s Ribosome,
With Spectinomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|2QOW|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOY|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
First 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QP0|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QAL|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAN|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QB9|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBB|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBD|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
First 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBF|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBH|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The First 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBJ|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The Second 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4K|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4M|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2VHO|C Chain C, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|C Chain C, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3DF3|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3J00|C Chain C, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|4ADV|C Chain C, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
pdb|3J0U|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|E Chain E, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
Length = 232
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170
A +IR+ I ++ G +IG G+++EKLR
Sbjct: 60 AKSIRVTIHTARPGIVIGKKGEDVEKLRK 88
>pdb|1VS5|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS7|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|3E1A|O Chain O, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Pre- Accommodation State
pdb|3E1C|O Chain O, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Post-Accommodation State
pdb|3I1M|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KC4|C Chain C, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be Found
In Pdb Entry 3kcr
pdb|3OR9|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The First
70s Ribosome.
pdb|3ORA|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3IZV|G Chain G, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Small Subunit Of A Ribosome Programmed With A
Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
Ef-Tu
pdb|3IZW|G Chain G, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding.This Entry Contains The
Small Subunit Of A Ribosome Programmed With A Cognate
Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
pdb|3SFS|C Chain C, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|C Chain C, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAQ|C Chain C, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|C Chain C, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 233
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170
A +IR+ I ++ G +IG G+++EKLR
Sbjct: 61 AKSIRVTIHTARPGIVIGKKGEDVEKLRK 89
>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 = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGE----QKHRHIQFGGS--AQQV 308
EM + E+LVG ++G+ G + + +GA I++ KGE ++R + GS A Q
Sbjct: 6 EMAVPENLVGAILGKGGKTLVEYQELTGARIQI-SKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 309 A--LAKQRVD 316
A L QRV
Sbjct: 65 AQYLISQRVT 74
>pdb|2GY9|C Chain C, Structure Of The 30s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYB|C Chain C, Structure Of The 30s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
pdb|3FIH|C Chain C, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 30s Subunit, Trnas And The Ternary
Complex.
pdb|2WWL|C Chain C, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 30s, The P-Site
Trna And The Tnac Leader Peptide (Part 1 Of 2).
pdb|3OFO|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFP|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3OFA|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OFB|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3OFX|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFY|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome
pdb|3OAQ|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OAR|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|2YKR|C Chain C, 30s Ribosomal Subunit With Rsga Bound In The Presence Of
Gmppnp
pdb|4A2I|C Chain C, Cryo-Electron Microscopy Structure Of The 30s Subunit In
Complex With The Yjeq Biogenesis Factor
pdb|3J18|C Chain C, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(30s Subunit)
pdb|4GD1|C Chain C, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4GD2|C Chain C, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 206
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170
A +IR+ I ++ G +IG G+++EKLR
Sbjct: 60 AKSIRVTIHTARPGIVIGKKGEDVEKLRK 88
>pdb|1X4M|A Chain A, Solution Structure Of Kh Domain In Far Upstream Element
Binding Protein 1
Length = 94
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202
++I S+AG +IG G+ I++L+ +G +V++ P A D+ ++I+GD
Sbjct: 19 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG--PQNTGA---DKPLRITGD 69
>pdb|1VIG|A Chain A, Nmr Study Of Vigilin, Repeat 6, 40 Structures
pdb|1VIH|A Chain A, Nmr Study Of Vigilin, Repeat 6, Minimized Average
Structure
Length = 71
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVA 309
DYV E+ I LIG+ G+NI+RI+++ +++ +K I+ G Q V
Sbjct: 5 DYV--EINIDHKFHRHLIGKSGANINRIKDQYKVSVRI--PPDSEKSNLIRIEGDPQGVQ 60
Query: 310 LAKQRVDE 317
AK+ + E
Sbjct: 61 QAKRELLE 68
>pdb|3O98|A Chain A, Glutathionylspermidine SynthetaseAMIDASE C59A COMPLEX WITH
ADP AND Gsp
pdb|3O98|B Chain B, Glutathionylspermidine SynthetaseAMIDASE C59A COMPLEX WITH
ADP AND Gsp
Length = 619
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQF 301
E++ + V + GRCGSNI + + + K G EQK+ + Q
Sbjct: 524 ELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQL 570
>pdb|2IO7|A Chain A, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND AMPPNP
pdb|2IO7|B Chain B, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND AMPPNP
pdb|2IO8|A Chain A, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND ADP
pdb|2IO8|B Chain B, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND ADP
pdb|2IO9|A Chain A, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ ,GSH AND ADP
pdb|2IO9|B Chain B, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ ,GSH AND ADP
pdb|2IOA|A Chain A, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND ADP AND
Phosphinate Inhibitor
pdb|2IOA|B Chain B, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE INCOMPLEX WITH MG2+ AND ADP AND
Phosphinate Inhibitor
pdb|2IOB|A Chain A, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE APO PROTEIN
pdb|2IOB|B Chain B, E. Coli Bifunctional Glutathionylspermidine
SynthetaseAMIDASE APO PROTEIN
Length = 619
Score = 27.7 bits (60), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 255 EMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQF 301
E++ + V + GRCGSNI + + + K G EQK+ + Q
Sbjct: 524 ELVKTGYAVKPIAGRCGSNIDLVSHHEEVLDKTSGKFAEQKNIYQQL 570
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
0.314 0.132 0.360
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,697,968
Number of Sequences: 62578
Number of extensions: 324593
Number of successful extensions: 689
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 86
length of query: 330
length of database: 14,973,337
effective HSP length: 99
effective length of query: 231
effective length of database: 8,778,115
effective search space: 2027744565
effective search space used: 2027744565
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)