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= 013530
(441 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AUA|A Chain A, Phosphatidylinositol Transfer Protein Sec14p From
Saccharomyces Cerevisiae
Length = 296
Score = 177 bits (450), Expect = 7e-45, Method: Compositional matrix adjust.
Identities = 100/262 (38%), Positives = 146/262 (55%), Gaps = 4/262 (1%)
Query: 70 DAAEEKAVNGFRNALIARDMLPSRHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENG 129
D+A+EKA+ R L + R DD T+LRFL+ARKFD+ +M+ WRK+ G
Sbjct: 27 DSAQEKALAELRKLLEDAGFI-ERLDD-STLLRFLRARKFDVQLAKEMFENCEKWRKDYG 84
Query: 130 VDTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVERFLKYH 189
DTI+QDF Y+E + YP YH DK+GRPVY E LG ++ ++ T+ ER LK
Sbjct: 85 TDTILQDFHYDEKPLIAKFYPQYYHKTDKDGRPVYFEELGAVNLHEMNKVTSEERMLKNL 144
Query: 190 VQGFEKTFSEKFPACSIAAKRHIDSTITILDVQGVNWMSFGKVAHDLVMRIQKIDGDNYP 249
V +E + PACS AA ++++ TI+D++G++ +S V I + YP
Sbjct: 145 VWEYESVVQYRLPACSRAAGHLVETSCTIMDLKGIS-ISSAYSVMSYVREASYISQNYYP 203
Query: 250 EILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFLGG 309
E + + +I+NA GF + K FLDP T +KI +LG + +LL+ I + LP GG
Sbjct: 204 ERMGKFYIINAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGG 263
Query: 310 TCSC-PNEGGCLKSNKGPWSDP 330
++GG S+ GPW DP
Sbjct: 264 KSEVDESKGGLYLSDIGPWRDP 285
>pdb|3B74|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylethanolamine
pdb|3B7N|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylinositol
pdb|3B7Q|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine
pdb|3B7Q|B Chain B, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine
pdb|3B7Z|A Chain A, Crystal Structure Of Yeast Sec14 Homolog Sfh1 In Complex
With Phosphatidylcholine Or Phosphatidylinositol
Length = 320
Score = 161 bits (408), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 98/269 (36%), Positives = 151/269 (56%), Gaps = 18/269 (6%)
Query: 73 EEKAVNGFRNALIARDMLPSRHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENGVDT 132
+E+A+ FR+ L+ ++ R DD T+LRFL+ARKFDI+ + +M+VE WR+E G +T
Sbjct: 39 QEEALLQFRSILLEKNY-KERLDD-STLLRFLRARKFDINASVEMFVETERWREEYGANT 96
Query: 133 IMQDFVYEEYDEVQ--------SCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVER 184
I++D YE E + YP YH VDK+GRP+Y E LG I+ K+ TT ++
Sbjct: 97 IIED--YENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQ 154
Query: 185 FLKYHVQGFEKTFSEKFPACSIAAKRHIDSTITILDVQGVNWMSFGKVAHDL--VMRIQK 242
L+ V+ +E + + PACS A I+++ T+LD++G+ S H L + +
Sbjct: 155 MLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGI---SLSNAYHVLSYIKDVAD 211
Query: 243 IDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQ 302
I + YPE + + +I+++ GF ++ K FLDP T +KI +LG + +LL+ I
Sbjct: 212 ISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIEN 271
Query: 303 LPDFLGGTCSCPNEG-GCLKSNKGPWSDP 330
LP GGT N S+ GPW DP
Sbjct: 272 LPVKYGGTSVLHNPNDKFYYSDIGPWRDP 300
>pdb|3Q8G|A Chain A, Resurrection Of A Functional Phosphatidylinositol Transfer
Protein From A Pseudo-Sec14 Scaffold By Directed
Evolution
Length = 320
Score = 159 bits (402), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 97/269 (36%), Positives = 150/269 (55%), Gaps = 18/269 (6%)
Query: 73 EEKAVNGFRNALIARDMLPSRHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENGVDT 132
+E+A+ FR+ L+ ++ R DD T+LRFL+ARKFDI+ + +M+VE WR+E G +T
Sbjct: 39 QEEALLQFRSILLEKNY-KERLDD-STLLRFLRARKFDINASVEMFVETERWREEYGANT 96
Query: 133 IMQDFVYEEYDEVQ--------SCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVER 184
I++D YE E + YP YH VDK+GRP+Y LG I+ K+ TT ++
Sbjct: 97 IIED--YENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFAELGGINLKKMYKITTEKQ 154
Query: 185 FLKYHVQGFEKTFSEKFPACSIAAKRHIDSTITILDVQGVNWMSFGKVAHDL--VMRIQK 242
L+ V+ +E + + PACS A I+++ T+LD++G+ S H L + +
Sbjct: 155 MLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGI---SLSNAYHVLSYIKDVAD 211
Query: 243 IDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQ 302
I + YPE + + +I+++ GF ++ K FLDP T +KI +LG + +LL+ I
Sbjct: 212 ISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIEN 271
Query: 303 LPDFLGGTCSCPNEG-GCLKSNKGPWSDP 330
LP GGT N S+ GPW DP
Sbjct: 272 LPVKYGGTSVLHNPNDKFYYSDIGPWRDP 300
>pdb|1OLM|E Chain E, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
Length = 403
Score = 96.3 bits (238), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 70/248 (28%), Positives = 124/248 (50%), Gaps = 15/248 (6%)
Query: 73 EEKAVNGFRNALIARDMLPS--RHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENGV 130
+++A+ FR + +D+LP+ DDY +LR+L+AR FD+ K+ M + + +RK+ +
Sbjct: 12 QKEALAKFRENV--QDVLPALPNPDDYF-LLRWLRARSFDLQKSEAMLRKHVEFRKQKDI 68
Query: 131 DTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVERFLKYHV 190
D I+ ++ + +Q G G D +G PV+ + +G +D L+ + + L+ +
Sbjct: 69 DNIIS---WQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKM 125
Query: 191 QGFEKTFSEKFPAC---SIAAKRHIDSTITILDVQGVNWMSFGKVAHDLVMRIQKIDGDN 247
+ E E C + R +++ I D +G+ K A + + +N
Sbjct: 126 RECELLLQE----CAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEEN 181
Query: 248 YPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFL 307
YPE L ++F+V A F + +N K FL T KI VLG + + LL+ I Q+P
Sbjct: 182 YPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEY 241
Query: 308 GGTCSCPN 315
GGT + P+
Sbjct: 242 GGTMTDPD 249
>pdb|1OLM|A Chain A, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
pdb|1OLM|C Chain C, Supernatant Protein Factor In Complex With
Rrr-Alpha-Tocopherylquinone: A Link Between Oxidized
Vitamin E And Cholesterol Biosynthesis
Length = 403
Score = 96.3 bits (238), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 70/248 (28%), Positives = 124/248 (50%), Gaps = 15/248 (6%)
Query: 73 EEKAVNGFRNALIARDMLPS--RHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENGV 130
+++A+ FR + +D+LP+ DDY +LR+L+AR FD+ K+ M + + +RK+ +
Sbjct: 12 QKEALAKFRENV--QDVLPALPNPDDYF-LLRWLRARSFDLQKSEAMLRKHVEFRKQKDI 68
Query: 131 DTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVERFLKYHV 190
D I+ ++ + +Q G G D +G PV+ + +G +D L+ + + L+ +
Sbjct: 69 DNIIS---WQPPEVIQQYLSGGMCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKM 125
Query: 191 QGFEKTFSEKFPAC---SIAAKRHIDSTITILDVQGVNWMSFGKVAHDLVMRIQKIDGDN 247
+ E E C + R +++ I D +G+ K A + + +N
Sbjct: 126 RECELLLQE----CAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCMFEEN 181
Query: 248 YPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFL 307
YPE L ++F+V A F + +N K FL T KI VLG + + LL+ I Q+P
Sbjct: 182 YPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIMVLGANWKEVLLKHISPDQVPVEY 241
Query: 308 GGTCSCPN 315
GGT + P+
Sbjct: 242 GGTMTDPD 249
>pdb|1O6U|A Chain A, The Crystal Structure Of Human Supernatant Protein Factor
pdb|1O6U|C Chain C, The Crystal Structure Of Human Supernatant Protein Factor
pdb|1O6U|E Chain E, The Crystal Structure Of Human Supernatant Protein Factor
Length = 403
Score = 92.0 bits (227), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 69/248 (27%), Positives = 121/248 (48%), Gaps = 15/248 (6%)
Query: 73 EEKAVNGFRNALIARDMLPS--RHDDYHTMLRFLKARKFDIDKTFQMWVEMLNWRKENGV 130
+++A+ FR + +D+LP+ DDY +LR+L+AR FD+ K+ + + +RK+ +
Sbjct: 12 QKEALAKFRENV--QDVLPALPNPDDYF-LLRWLRARSFDLQKSEAXLRKHVEFRKQKDI 68
Query: 131 DTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTTVERFLKYHV 190
D I+ ++ + +Q G G D +G PV+ + +G +D L+ + + L+
Sbjct: 69 DNIIS---WQPPEVIQQYLSGGXCGYDLDGCPVWYDIIGPLDAKGLLFSASKQDLLRTKX 125
Query: 191 QGFEKTFSEKFPAC---SIAAKRHIDSTITILDVQGVNWMSFGKVAHDLVMRIQKIDGDN 247
+ E E C + R +++ I D +G+ K A + +N
Sbjct: 126 RECELLLQE----CAHQTTKLGRKVETITIIYDCEGLGLKHLWKPAVEAYGEFLCXFEEN 181
Query: 248 YPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFL 307
YPE L ++F+V A F + +N K FL T KI VLG + + LL+ I Q+P
Sbjct: 182 YPETLKRLFVVKAPKLFPVAYNLIKPFLSEDTRKKIXVLGANWKEVLLKHISPDQVPVEY 241
Query: 308 GGTCSCPN 315
GGT + P+
Sbjct: 242 GGTXTDPD 249
>pdb|1OIP|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-tocopherol Transfer Protein
pdb|1OIZ|A Chain A, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
pdb|1OIZ|B Chain B, The Molecular Basis Of Vitamin E Retention: Structure Of
Human Alpha-Tocopherol Transfer Protein
Length = 278
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 50/212 (23%), Positives = 85/212 (40%), Gaps = 26/212 (12%)
Query: 100 MLRFLKARKFDIDKTFQMWVEMLNWRKENGVDTIMQDFVYEEYDEVQSCYPHGYHGV--- 156
+LRFL+AR FD+D +++ WR E I D + GYHGV
Sbjct: 52 LLRFLRARDFDLDLAWRLLKNYYKWRAE--CPEISADL---HPRSIIGLLKAGYHGVLRS 106
Query: 157 -DKEGRPVYIERLGQIDPSKLMSCTTVERFLKYHVQGFEKTFSEKFPACSIAAKRHIDST 215
D G V I R+ DP K+ + V R + + + +R +
Sbjct: 107 RDPTGSKVLIYRIAHWDP-KVFTAYDVFRV---------SLITSELIVQEVETQR--NGI 154
Query: 216 ITILDVQGVNWMSFGKVAHDLVMRIQKIDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFL 275
I D++G + ++ + +I + D++P + + ++N F V++ K FL
Sbjct: 155 KAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSMIKPFL 214
Query: 276 DPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFL 307
K +I + G + LL+ PD L
Sbjct: 215 TEKIKERIHMHGNNYKQSLLQ-----HFPDIL 241
>pdb|1R5L|A Chain A, Crystal Structure Of Human Alpha-tocopherol Transfer
Protein Bound To Its Ligand
Length = 262
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 50/212 (23%), Positives = 84/212 (39%), Gaps = 26/212 (12%)
Query: 100 MLRFLKARKFDIDKTFQMWVEMLNWRKENGVDTIMQDFVYEEYDEVQSCYPHGYHGV--- 156
+LRFL+AR FD+D +++ WR E I D + GYHGV
Sbjct: 36 LLRFLRARDFDLDLAWRLLKNYYKWRAE--CPEISADL---HPRSIIGLLKAGYHGVLRS 90
Query: 157 -DKEGRPVYIERLGQIDPSKLMSCTTVERFLKYHVQGFEKTFSEKFPACSIAAKRHIDST 215
D G V I R+ DP K+ + V R + + + +R +
Sbjct: 91 RDPTGSKVLIYRIAHWDP-KVFTAYDVFRV---------SLITSELIVQEVETQR--NGI 138
Query: 216 ITILDVQGVNWMSFGKVAHDLVMRIQKIDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFL 275
I D++G + ++ + +I + D++P + + ++N F V++ K FL
Sbjct: 139 KAIFDLEGWQFSHAFQITPSVAKKIAAVLTDSFPLKVRGIHLINEPVIFHAVFSXIKPFL 198
Query: 276 DPKTTAKIQVLGYKFHDKLLEVIDSSQLPDFL 307
K +I G + LL+ PD L
Sbjct: 199 TEKIKERIHXHGNNYKQSLLQ-----HFPDIL 225
>pdb|3HY5|A Chain A, Crystal Structure Of Cralbp
Length = 316
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 45/249 (18%), Positives = 103/249 (41%), Gaps = 20/249 (8%)
Query: 64 SIEDVRDAAEEKAVNGFRNALIARDMLPSRHDDYHTMLRFLKARKFDIDKTFQMWVEMLN 123
++ ++++ + +A +G A+ + + + + LRF++ARKF++ + +++ +N
Sbjct: 61 AVRELQEMVQAQAASGEELAVAVAERVQEKDSGF--FLRFIRARKFNVGRAYELLRGYVN 118
Query: 124 WRKE--NGVDTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTT 181
+R + D++ + V +++ YP DK GR V + + ++ T
Sbjct: 119 FRLQYPELFDSLSPEAV---RCTIEAGYPGVLSSRDKYGRVVMLFNIENWQSQEI----T 171
Query: 182 VERFLKYHVQGFEKTFSEKFPACSIAAKRHIDSTITILDVQGVNWMSFGKVAHDLVMRIQ 241
+ L+ + EK + + I+ I + +G + + ++
Sbjct: 172 FDEILQAYCFILEKLLENE--------ETQINGFCIIENFKGFTMQQAASLRTSDLRKMV 223
Query: 242 KIDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDSS 301
+ D++P + ++ F +N K FL K ++ V G + ID +
Sbjct: 224 DMLQDSFPARFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDL-SGFYQEIDEN 282
Query: 302 QLPDFLGGT 310
LP GGT
Sbjct: 283 ILPSDFGGT 291
>pdb|3HX3|A Chain A, Crystal Structure Of Cralbp Mutant R234w
Length = 316
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 47/250 (18%), Positives = 103/250 (41%), Gaps = 22/250 (8%)
Query: 64 SIEDVRDAAEEKAVNGFRNALIARDMLPSRHDDYHTMLRFLKARKFDIDKTFQMWVEMLN 123
++ ++++ + +A +G A+ + + + + LRF++ARKF++ + +++ +N
Sbjct: 61 AVRELQEXVQAQAASGEELAVAVAERVQEKDSGF--FLRFIRARKFNVGRAYELLRGYVN 118
Query: 124 WRKE--NGVDTIMQDFVYEEYDEVQSCYPHGYHGVDKEGRPVYIERLGQIDPSKLMSCTT 181
+R + D++ + V +++ YP DK GR V + + ++ T
Sbjct: 119 FRLQYPELFDSLSPEAV---RCTIEAGYPGVLSSRDKYGRVVXLFNIENWQSQEI----T 171
Query: 182 VERFLKYHVQGFEKTFSEKFPACSIAAKRHIDSTITILDVQGVNWMSFGKV-AHDLVMRI 240
+ L+ + EK + + I+ I + +G + DL +
Sbjct: 172 FDEILQAYCFILEKLLENE--------ETQINGFCIIENFKGFTXQQAASLRTSDLRKXV 223
Query: 241 QKIDGDNYPEILHQMFIVNAGSGFKLVWNTAKGFLDPKTTAKIQVLGYKFHDKLLEVIDS 300
+ D++P + ++ F +N K FL K ++ V G + ID
Sbjct: 224 DXLQ-DSFPAWFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDL-SGFYQEIDE 281
Query: 301 SQLPDFLGGT 310
+ LP GGT
Sbjct: 282 NILPSDFGGT 291
>pdb|3MTJ|A Chain A, The Crystal Structure Of A Homoserine Dehydrogenase From
Thiobacillus Denitrificans To 2.15a
Length = 444
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 396 GRMSEPTSTSSVAEQTDVAGVHEAISTNRLPH 427
G SEPT+++ VA+ DV +H A +R+PH
Sbjct: 306 GAGSEPTASAVVADLVDVTRLHTADPHHRVPH 337
>pdb|1P85|F Chain F, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P86|F Chain F, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AW4|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AWB|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 50s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|1VS6|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS8|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2GYA|F Chain F, Structure Of The 50s 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|2GYC|F Chain F, Structure Of The 50s 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|2I2T|H Chain H, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2V|H Chain H, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2J28|H Chain H, Model Of E. Coli Srp Bound To 70s Rncs
pdb|2QOV|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The First 70s Ribosome.
The Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|2QOX|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The Second 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QOZ|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
First 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QP1|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QAM|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAO|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBA|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBC|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBE|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2VHM|H Chain H, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 1 Of 4)
pdb|2VHN|H Chain H, Structure Of Pdf Binding Helix In Complex With The
Ribosome. (Part 2 Of 4)
pdb|2RDO|H Chain H, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|3DF2|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 50s Subunit Of The First 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|3DF4|H Chain H, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 50s Subunit Of The Second 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes.
pdb|3BBX|H Chain H, The Hsp15 Protein Fitted Into The Low Resolution Cryo-Em
Map 50s.Nc-Trna.Hsp15 Complex
pdb|3FIK|H Chain H, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|3E1B|4 Chain 4, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|4 Chain 4, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
pdb|3I1N|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1P|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1R|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1T|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I20|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I22|H Chain H, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KCR|H Chain H, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
pdb|2WWQ|H Chain H, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 50s, The P-Site
Trna And The Tnac Leader Peptide (Part 2 Of 2).
pdb|1VT2|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3ORB|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The First
70s Ribosome Bound To Cem-101.
pdb|3OFQ|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OFR|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
First 70s Ribosome With Erthromycin Bound.
pdb|3OFC|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The First 70s Ribosome With Chloramphenicol Bound.
pdb|3OFD|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OFZ|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
First 70s Ribosome Bound To Clindamycin.
pdb|3OG0|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAS|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAT|H Chain H, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of The
First 70s Ribosome With Telithromycin Bound.
pdb|3IZT|I Chain I, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A
Near-Cognate Codon.
pdb|3IZU|I Chain I, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A Cognate
Codon
pdb|3J01|H Chain H, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3R8S|H Chain H, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3R8T|H Chain H, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3J0T|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|I Chain I, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J19|H Chain H, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(50s Subunit)
pdb|4GAR|H Chain H, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAU|H Chain H, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 149
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 47/102 (46%), Gaps = 19/102 (18%)
Query: 335 LVHAGNAMCSRKTKRSSDF-----DDLEIKL---FSSKVANSEKSSADSTLDVRSNTSGF 386
LV G A+ + TK++ +F +LE KL ++ A +EK +A T+ + S
Sbjct: 30 LVPQGKAVPA--TKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAG-- 85
Query: 387 IKLVPLNDNGRMSEPTSTSSVAEQTDVAGVHEAISTNRLPHG 428
D G++ T +A+ AGV A S RLP+G
Sbjct: 86 -------DEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG 120
>pdb|2P0A|A Chain A, The Crystal Structure Of Human Synapsin Iii (Syn3) In
Complex With Amppnp
pdb|2P0A|B Chain B, The Crystal Structure Of Human Synapsin Iii (Syn3) In
Complex With Amppnp
Length = 344
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 26/56 (46%)
Query: 330 PGIMKLVHAGNAMCSRKTKRSSDFDDLEIKLFSSKVANSEKSSADSTLDVRSNTSG 385
P ++KL HA M K + DF D+ + +K + ++ DS D+R G
Sbjct: 171 PVVVKLGHAHAGMGKIKVENQLDFQDITSVVAMAKTYATTEAFIDSKYDIRIQKIG 226
>pdb|1M9W|A Chain A, Study Of Electrostatic Potential Surface Distribution
Using High Resolution Side-Chain Conformation Determined
By Nmr
Length = 98
Score = 28.1 bits (61), Expect = 9.6, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 24/51 (47%)
Query: 214 STITILDVQGVNWMSFGKVAHDLVMRIQKIDGDNYPEILHQMFIVNAGSGF 264
ST+TI + V W++ H++V +D D ++ H+ AG F
Sbjct: 19 STVTIKAGEEVKWVNNKLSPHNIVFAADGVDADTAAKLSHKGLAFAAGESF 69
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,966,032
Number of Sequences: 62578
Number of extensions: 487200
Number of successful extensions: 1084
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1055
Number of HSP's gapped (non-prelim): 18
length of query: 441
length of database: 14,973,337
effective HSP length: 102
effective length of query: 339
effective length of database: 8,590,381
effective search space: 2912139159
effective search space used: 2912139159
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)