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= 022514
(296 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 304
Score = 463 bits (1192), Expect = e-131, Method: Compositional matrix adjust.
Identities = 225/290 (77%), Positives = 247/290 (85%), Gaps = 3/290 (1%)
Query: 2 AFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDII 61
FVK QK+ AYFKRFQVK+KRRR+GKTDYRARIRL NQDKNKYNTPKYRFV TNKDI
Sbjct: 6 GFVKTQKTHAYFKRFQVKFKRRRQGKTDYRARIRLTNQDKNKYNTPKYRFV---TNKDIT 62
Query: 62 AQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEG 121
AQIV A I GD V+AAAY+HELPRYGLEVGLTNYAAAYCTGLLLARRVL + +D EYEG
Sbjct: 63 AQIVYATIAGDIVMAAAYSHELPRYGLEVGLTNYAAAYCTGLLLARRVLTLRGLDQEYEG 122
Query: 122 NVEATGEDYSVEPADTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAG 181
NVEATGEDY VEPAD RRPFRALLDVGLI+TTTGNRVF IPHSDKRFAG
Sbjct: 123 NVEATGEDYYVEPADERRPFRALLDVGLIRTTTGNRVFGALKGALDGGLDIPHSDKRFAG 182
Query: 182 FSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKK 241
F KD KQLD+++HRKYIYGGHVA YM ++ E+EPEK+Q+HF+EY+KKGIDADG+E+LYKK
Sbjct: 183 FKKDEKQLDSDIHRKYIYGGHVADYMRSMAEEEPEKFQAHFSEYLKKGIDADGMESLYKK 242
Query: 242 VHAAIRADPTMKKSEKPAPKEHKRYNLKKLTYEERKAKLVERLNALNSAV 291
VHAAIRADPTM KS K P HKRYNLKKLTYE+RKA LVERLNALNS+
Sbjct: 243 VHAAIRADPTMAKSTKKEPATHKRYNLKKLTYEQRKASLVERLNALNSSA 292
>pdb|2ZKR|NN Chain n, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 297
Score = 286 bits (731), Expect = 1e-77, Method: Compositional matrix adjust.
Identities = 153/284 (53%), Positives = 199/284 (70%), Gaps = 2/284 (0%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M FVK K+KAYFKR+QVK++RRREGKTDY AR RL+ QDKNKYNTPKYR +VR TN+DI
Sbjct: 1 MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI 60
Query: 61 IAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120
I QI A I GD ++ A YAHELP+YG++VGLTNYAAAYCTGLLLARR+L MD YE
Sbjct: 61 ICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE 120
Query: 121 GNVEATGEDYSVEPADTR-RPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRF 179
G VE TG++Y+VE D + F LD GL +TTTGN+VF IPHS KRF
Sbjct: 121 GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF 180
Query: 180 AGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALY 239
G+ + K+ +AEVHRK+I G +VA YM LME++ + Y+ F++YIK + D +E +Y
Sbjct: 181 PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY 240
Query: 240 KKVHAAIRADPTMKKSEKPAPKEHKRYNLKKLTYEERKAKLVER 283
KK HAAIR +P +K K + KR+N K++ ++K ++ ++
Sbjct: 241 KKAHAAIRENPVYEKKPK-KEVKKKRWNRPKMSLAQKKDRVAQK 283
>pdb|3U5E|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|D Chain D, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 297
Score = 281 bits (720), Expect = 3e-76, Method: Compositional matrix adjust.
Identities = 149/282 (52%), Positives = 184/282 (65%), Gaps = 6/282 (2%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
MAF K KS AY RFQ ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 61 IAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120
I QI+S+ I GD VLAAAY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D+ Y+
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK 120
Query: 121 GNVEATGEDYSVEPA-DTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRF 179
G E GE E D RPF+ LD+GL +TTTG RVF +PHS+ RF
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF 180
Query: 180 AGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALY 239
G+ + +++D E+ R YI+GGHV+ YM L +D+ E++ F Y+ IDAD LE +Y
Sbjct: 181 PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY 240
Query: 240 KKVHAAIRADPTMKKSEKPAPKEH-----KRYNLKKLTYEER 276
H AIRADP K +EK KE K+Y KL+ EER
Sbjct: 241 TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEER 282
>pdb|3IZS|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 297
Score = 281 bits (720), Expect = 3e-76, Method: Compositional matrix adjust.
Identities = 149/282 (52%), Positives = 184/282 (65%), Gaps = 6/282 (2%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
MAF K KS AY RFQ ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 61 IAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120
I QI+S+ I GD VLAAAY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D+ Y+
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYK 120
Query: 121 GNVEATGEDYSVEPA-DTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRF 179
G E GE E D RPF+ LD+GL +TTTG RVF +PHS+ RF
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF 180
Query: 180 AGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALY 239
G+ + +++D E+ R YI+GGHV+ YM L +D+ E++ F Y+ IDAD LE +Y
Sbjct: 181 PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY 240
Query: 240 KKVHAAIRADPTMKKSEKPAPKEH-----KRYNLKKLTYEER 276
H AIRADP K +EK KE K+Y KL+ EER
Sbjct: 241 TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEER 282
>pdb|3ZF7|UU Chain u, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 308
Score = 279 bits (714), Expect = 1e-75, Method: Compositional matrix adjust.
Identities = 145/287 (50%), Positives = 192/287 (66%), Gaps = 12/287 (4%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M FVK K+KAY+KRFQVKY+RRREGKTDY AR R++ QDK K+ TPKYR VVR TN+D+
Sbjct: 1 MTFVKVVKNKAYYKRFQVKYRRRREGKTDYHARRRMVLQDKTKFGTPKYRLVVRITNRDV 60
Query: 61 IAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120
IAQIV A +VGD V+ AAY+HELP +G+E GLTNYAAAY TGLL+ARR+L L + +++
Sbjct: 61 IAQIVHAKVVGDEVVMAAYSHELPLFGIEHGLTNYAAAYATGLLVARRMLAKLGLAEKFV 120
Query: 121 GNVEATGEDYSVEPAD-------TRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIP 173
G E G +V D +R PF+A+LDVGL +TTTG RVF +P
Sbjct: 121 GVKEVDGSYAAVRTKDDDQGDDESRFPFKAILDVGLARTTTGARVFGVLKGAVDGGLAVP 180
Query: 174 HSDKRFAGFSKDGKQLDAEVHRKYIYGGHVAAYMSTLMED---EPEKYQSHFTEYIKKGI 230
H RF G++K+ L+A+VHR I+G HVA Y+ + E+ P++ F+++I +
Sbjct: 181 HRPNRFPGYNKESDALNAKVHRDRIFGRHVADYLKQVREEASSNPDEKTCQFSKFIAAKV 240
Query: 231 DADGLEALYKKVHAAIRADPTMK--KSEKPAPKEHKRYNLKKLTYEE 275
D +E +YK+ HAAIRADPT + K E+PA + K+YN KLT E
Sbjct: 241 SPDDMEGMYKRAHAAIRADPTKRRAKKERPAEAKPKKYNTVKLTGAE 287
>pdb|4A17|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 301
Score = 249 bits (637), Expect = 9e-67, Method: Compositional matrix adjust.
Identities = 138/292 (47%), Positives = 185/292 (63%), Gaps = 13/292 (4%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M FVK K+KAYFKRFQ KY+RRREG TDY AR RLI QDK+KYNTPKYR V R TN I
Sbjct: 1 MGFVKVLKTKAYFKRFQTKYRRRREGLTDYYARKRLIIQDKDKYNTPKYRLVARATNTRI 60
Query: 61 IAQIVSANIVGDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYE 120
IAQIV A + D VL AA ++EL R+G+ GL +YAAAY TGLLLARR+LK + +D Y
Sbjct: 61 IAQIVYATLKCDRVLCAADSYELKRFGVSTGLASYAAAYATGLLLARRLLKQIGLDTVYA 120
Query: 121 GNVEATGEDYSV-EPADTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRF 179
G + G ++V E ++PF+A+LD GL++TTTGNRVF IPHS+ RF
Sbjct: 121 GQTKVDGAYFNVDEDQKEKKPFKAILDAGLVRTTTGNRVFGVLKGACDGGINIPHSESRF 180
Query: 180 AGFSK-----DGKQLDAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIK--KGIDA 232
G+ + + + E H+ I+G H+ AYM L E +Q F+++ K +
Sbjct: 181 PGYVRASDEGESSKYKPEDHKARIFGKHIDAYMKHLKGQSNEAFQKQFSKWSKTLEAAKV 240
Query: 233 DGLEALYKKVHAAIRADP----TMKKSEKPAPKEHKRYNLKKLTYEERKAKL 280
D +E L+ KVHA IR +P + KK++KP ++HK++ KLT +RK ++
Sbjct: 241 DSVEKLFTKVHAEIRKNPERVKSTKKNDKP-KRDHKKFYPTKLTAAQRKDRV 291
>pdb|3JYW|E Chain E, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 237
Score = 249 bits (636), Expect = 1e-66, Method: Compositional matrix adjust.
Identities = 127/237 (53%), Positives = 159/237 (67%), Gaps = 1/237 (0%)
Query: 11 AYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIV 70
AY RFQ ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDII QI+S+ I
Sbjct: 1 AYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTIT 60
Query: 71 GDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDY 130
GD VLAAAY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D+ Y+G E GE
Sbjct: 61 GDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYE 120
Query: 131 SVEPA-DTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQL 189
E D RPF+ LD+GL +TTTG RVF +PHS+ RF G+ + +++
Sbjct: 121 LTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEI 180
Query: 190 DAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKVHAAI 246
D E+ R YI+GGHV+ YM L +D+ E++ F Y+ IDAD LE +Y H AI
Sbjct: 181 DPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAI 237
>pdb|1S1I|E Chain E, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 222
Score = 233 bits (594), Expect = 9e-62, Method: Compositional matrix adjust.
Identities = 119/222 (53%), Positives = 150/222 (67%), Gaps = 1/222 (0%)
Query: 11 AYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIV 70
AY RFQ ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDII QI+S+ I
Sbjct: 1 AYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTIT 60
Query: 71 GDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDY 130
GD VLAAAY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D+ Y+G E GE
Sbjct: 61 GDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYE 120
Query: 131 SVEPA-DTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQL 189
E D RPF+ LD+GL +TTTG RVF +PHS+ RF G+ + +++
Sbjct: 121 LTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEI 180
Query: 190 DAEVHRKYIYGGHVAAYMSTLMEDEPEKYQSHFTEYIKKGID 231
D E+ R YI+GGHV+ YM L +D+ E++ F Y+ ID
Sbjct: 181 DPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDID 222
>pdb|1S72|N Chain N, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|N Chain N, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|N Chain N, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|N Chain N, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|N Chain N, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|N Chain N, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|N Chain N, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|N Chain N, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|N Chain N, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|N Chain N, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|N Chain N, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|N Chain N, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|N Chain N, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|N Chain N, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|N Chain N, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|N Chain N, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|N Chain N, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|N Chain N, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|N Chain N, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|N Chain N, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|N Chain N, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|N Chain N, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|N Chain N, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|N Chain N, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|N Chain N, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|N Chain N, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|M Chain M, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|N Chain N, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|N Chain N, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|N Chain N, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|N Chain N, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|N Chain N, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|N Chain N, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 187
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 70/233 (30%), Positives = 95/233 (40%), Gaps = 60/233 (25%)
Query: 11 AYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIV 70
A R++V +RRRE +TDY R+RL+ K R V R +NK + AQ+V+
Sbjct: 2 ATGPRYKVPMRRRREARTDYHQRLRLLKSGKP-------RLVARKSNKHVRAQLVTLGPN 54
Query: 71 GDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDY 130
GD LA+A++ +L YG E N +AY TGLL R E VE
Sbjct: 55 GDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRA---------QEAGVE------ 99
Query: 131 SVEPADTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQLD 190
A+LD+GL T G++VF IPH+D A + +
Sbjct: 100 -----------EAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQR------ 142
Query: 191 AEVHRKYIYGGHVAAYMSTLME----------DEPEKYQSHFTEYIKKGIDAD 233
G H+A Y L E D PE HF E + +D D
Sbjct: 143 -------TRGAHIAEYDEQLEEPLYSGDFDAADLPE----HFDELRETLLDGD 184
>pdb|1FFK|K Chain K, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|Q Chain Q, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1JJ2|M Chain M, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|M Chain M, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|O Chain O, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|O Chain O, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|O Chain O, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|O Chain O, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|O Chain O, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|QQ Chain q, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|O Chain O, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|O Chain O, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|O Chain O, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|O Chain O, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|O Chain O, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|O Chain O, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|O Chain O, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|O Chain O, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|M Chain M, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|M Chain M, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|M Chain M, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YL3|Q Chain Q, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|S Chain S, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf1, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400
pdb|2B9N|S Chain S, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf2, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400.
pdb|2B9P|S Chain S, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex With
Trnas And Mrna With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|3CXC|M Chain M, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3G4S|N Chain N, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|N Chain N, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|N Chain N, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|M Chain M, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 186
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 70/233 (30%), Positives = 95/233 (40%), Gaps = 60/233 (25%)
Query: 11 AYFKRFQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIV 70
A R++V +RRRE +TDY R+RL+ K R V R +NK + AQ+V+
Sbjct: 1 ATGPRYKVPMRRRREARTDYHQRLRLLKSGKP-------RLVARKSNKHVRAQLVTLGPN 53
Query: 71 GDSVLAAAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDY 130
GD LA+A++ +L YG E N +AY TGLL R E VE
Sbjct: 54 GDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRA---------QEAGVE------ 98
Query: 131 SVEPADTRRPFRALLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQLD 190
A+LD+GL T G++VF IPH+D A + +
Sbjct: 99 -----------EAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQR------ 141
Query: 191 AEVHRKYIYGGHVAAYMSTLME----------DEPEKYQSHFTEYIKKGIDAD 233
G H+A Y L E D PE HF E + +D D
Sbjct: 142 -------TRGAHIAEYDEQLEEPLYSGDFDAADLPE----HFDELRETLLDGD 183
>pdb|3J21|O Chain O, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 203
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 63/223 (28%), Positives = 93/223 (41%), Gaps = 47/223 (21%)
Query: 25 EGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIIAQIVSANIVGDSVLAAAYAHELP 84
EGKT+YR R++L+ K R VVR + IAQI+ + GD L +A+ EL
Sbjct: 16 EGKTNYRKRLKLLKSGKP-------RLVVRKSLNHHIAQIIVYDPKGDRTLVSAHTRELI 68
Query: 85 R-YGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDYSVEPADTRRPFRA 143
R +G + N +AY GLL+ Y + A A
Sbjct: 69 RDFGWKGHCGNTPSAYLLGLLIG-----------------------YKAKQAGIE---EA 102
Query: 144 LLDVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQLDAEVHRKYIYGGHV 203
+LD+GL G+ VF +PHS + F + I G H+
Sbjct: 103 ILDIGLHPPVRGSSVFAVLKGAVDAGLNVPHSPEIFPDEYR-------------IRGEHI 149
Query: 204 AAYMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKVHAAI 246
A Y L E + EK++ F Y+ KG+D + L +++V A I
Sbjct: 150 AEYAKMLKEQDEEKFRRQFGGYLVKGLDPEKLPEHFEEVKARI 192
>pdb|4GMN|B Chain B, Structural Basis Of Rpl5 Recognition By Syo1
Length = 49
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/41 (65%), Positives = 31/41 (75%)
Query: 1 MAFVKAQKSKAYFKRFQVKYKRRREGKTDYRARIRLINQDK 41
MAF K K+ AY+ RFQ K+KRRR+GKTDY AR RLI Q K
Sbjct: 1 MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAK 41
>pdb|1I3Q|I Chain I, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|I Chain I, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|I Chain I, Rna Polymerase Ii Elongation Complex
pdb|1K83|I Chain I, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|I Chain I, Wild Type Rna Polymerase Ii
pdb|1NT9|I Chain I, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|I Chain I, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|I Chain I, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|I Chain I, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|I Chain I, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|I Chain I, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|I Chain I, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|I Chain I, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|I Chain I, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|I Chain I, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|I Chain I, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|I Chain I, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|I Chain I, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|I Chain I, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|I Chain I, 12-Subunit Rna Polymerase Ii
pdb|2E2H|I Chain I, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|I Chain I, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|I Chain I, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|U Chain U, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|I Chain I, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|I Chain I, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|I Chain I, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|I Chain I, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|I Chain I, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|I Chain I, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|I Chain I, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|I Chain I, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|I Chain I, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|I Chain I, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|I Chain I, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|I Chain I, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|J Chain J, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|I Chain I, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|U Chain U, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|I Chain I, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|I Chain I, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|I Chain I, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|I Chain I, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|I Chain I, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|I Chain I, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|I Chain I, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|I Chain I, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|I Chain I, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3RZD|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|I Chain I, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|I Chain I, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|I Chain I, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|I Chain I, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|I Chain I, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|I Chain I, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|I Chain I, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|I Chain I, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|I Chain I, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 122
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 246 IRADPTMKKSEKPAPKEHKRYNLKKLTYEERK 277
I +DPT+ +S++ PK H R N+ + + RK
Sbjct: 62 IGSDPTLPRSDRECPKCHSRENVFFQSQQRRK 93
>pdb|1VZ0|A Chain A, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|B Chain B, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|C Chain C, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|D Chain D, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|E Chain E, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|F Chain F, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|G Chain G, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
pdb|1VZ0|H Chain H, Chromosome Segregation Protein Spo0j From Thermus
Thermophilus
Length = 230
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 37/160 (23%), Positives = 57/160 (35%), Gaps = 15/160 (9%)
Query: 86 YGLEVGLTNYAAAYCTGLLLARRVLKMLEMDDEYEGNVEATGEDYSVEPADTRRPFRALL 145
Y L G Y AA GL V+K L + E + + + P + R ++ALL
Sbjct: 72 YELVAGERRYRAALMAGLQEVPAVVKDLTDREALELALVENLQREDLSPVEEARGYQALL 131
Query: 146 DVGLIKTTTGNRVFXXXXXXXXXXXXIPHSDKRFAGFSKDGKQLDAEVHRKYIYGGHVAA 205
++GL + RV + QL E G A
Sbjct: 132 EMGLTQEEVARRVGKARSTVANALRLL---------------QLPPEALEALERGEITAG 176
Query: 206 YMSTLMEDEPEKYQSHFTEYIKKGIDADGLEALYKKVHAA 245
+ L+ EPE E ++KG+ EAL +++ A
Sbjct: 177 HARALLMLEPEDRLWGLKEILEKGLSVRQAEALRERLAMA 216
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
0.317 0.134 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,382,258
Number of Sequences: 62578
Number of extensions: 339531
Number of successful extensions: 981
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 943
Number of HSP's gapped (non-prelim): 20
length of query: 296
length of database: 14,973,337
effective HSP length: 98
effective length of query: 198
effective length of database: 8,840,693
effective search space: 1750457214
effective search space used: 1750457214
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: 51 (24.3 bits)