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= psy1114
(480 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|HH Chain h, 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 = 214
Score = 310 bits (794), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 146/191 (76%), Positives = 169/191 (88%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YRYCKNKPYPKSRFCRGVPD KIRIFDLG+KKAKV++FPLC H+VSDEYEQLSSE
Sbjct: 4 RPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSE 63
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RIC NKY+VK+CGKD FHIR+RLHPFHVIRINKMLSCAGADRLQTGMRGA+GKPQ
Sbjct: 64 ALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQ 123
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYET 250
GTVA+V+IGQ IMS+R+ + K VIEALRRAKFKFPGRQKI++SKKWGFTK++ +E+E
Sbjct: 124 GTVAKVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEN 183
Query: 251 LRDQNRILHDA 261
+ + R++ D
Sbjct: 184 MVAEKRLIPDG 194
Score = 197 bits (501), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 91/109 (83%), Positives = 99/109 (90%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YRYCKNKPYPKSRFCRGVPD KIRIFDLG+KKAKV++FPLC H+VSDEYEQLSSE
Sbjct: 4 RPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSE 63
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RIC NKY+VK+CGKD FHIR+RLHPFHVIRINKMLSCAGADR +
Sbjct: 64 ALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQ 112
Score = 117 bits (292), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 69/143 (48%), Positives = 92/143 (64%), Gaps = 5/143 (3%)
Query: 201 PIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRILHD 260
P+ SD+++ EAL A+ + + K GF R + N++L
Sbjct: 47 PLCGHMVSDEYEQLSSEALEAARI-CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSC 105
Query: 261 AHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPG 320
A D RLQTGMRGA+GKPQGTVA+V+IGQ IMS+R+ + K VIEALRRAKFKFPG
Sbjct: 106 AGAD----RLQTGMRGAFGKPQGTVAKVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPG 161
Query: 321 RQKIYVSKKWGFTKYDREEYETL 343
RQKI++SKKWGFTK++ +E+E +
Sbjct: 162 RQKIHISKKWGFTKFNADEFENM 184
Score = 106 bits (265), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 49/70 (70%), Positives = 62/70 (88%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGTVA+V+IGQ IMS+R+ + K VIEALRRAKFKFPGRQKI++SKKWGFT
Sbjct: 115 MRGAFGKPQGTVAKVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFT 174
Query: 61 KYDREEYETL 70
K++ +E+E +
Sbjct: 175 KFNADEFENM 184
>pdb|3IZR|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 224
Score = 278 bits (711), Expect = 5e-75, Method: Compositional matrix adjust.
Identities = 132/191 (69%), Positives = 153/191 (80%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YR KNKPYPKSR+CRGVPDPKIRI+D+G KK V++FP CVHLVS E E +SSE
Sbjct: 4 RPARCYRQIKNKPYPKSRYCRGVPDPKIRIYDVGMKKKGVDEFPYCVHLVSWEKENVSSE 63
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RI CNKY+ KN GKD FH+R+R+HPFHV+RINKMLSCAGADRLQTGMRGA+GKPQ
Sbjct: 64 ALEAARIACNKYMTKNAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPQ 123
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYET 250
GT ARV+IGQ ++SVR + EALRRAKFKFPGRQKI S+KWGFTK+ REEY
Sbjct: 124 GTCARVDIGQVLLSVRCKESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFTKFTREEYVK 183
Query: 251 LRDQNRILHDA 261
L+ + RI+ D
Sbjct: 184 LKAEGRIMSDG 194
Score = 172 bits (435), Expect = 5e-43, Method: Compositional matrix adjust.
Identities = 78/109 (71%), Positives = 90/109 (82%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YR KNKPYPKSR+CRGVPDPKIRI+D+G KK V++FP CVHLVS E E +SSE
Sbjct: 4 RPARCYRQIKNKPYPKSRYCRGVPDPKIRIYDVGMKKKGVDEFPYCVHLVSWEKENVSSE 63
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RI CNKY+ KN GKD FH+R+R+HPFHV+RINKMLSCAGADR +
Sbjct: 64 ALEAARIACNKYMTKNAGKDAFHLRVRVHPFHVLRINKMLSCAGADRLQ 112
Score = 107 bits (268), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 56/93 (60%), Positives = 67/93 (72%), Gaps = 4/93 (4%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQTGMRGA+GKPQGT ARV+IGQ ++SVR + EALRRA
Sbjct: 100 NKMLSCAGAD----RLQTGMRGAFGKPQGTCARVDIGQVLLSVRCKESNAKHAEEALRRA 155
Query: 315 KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 347
KFKFPGRQKI S+KWGFTK+ REEY L+ +
Sbjct: 156 KFKFPGRQKIIHSRKWGFTKFTREEYVKLKAEG 188
Score = 97.1 bits (240), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 47/74 (63%), Positives = 56/74 (75%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGT ARV+IGQ ++SVR + EALRRAKFKFPGRQKI S+KWGFT
Sbjct: 115 MRGAFGKPQGTCARVDIGQVLLSVRCKESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFT 174
Query: 61 KYDREEYETLRDQN 74
K+ REEY L+ +
Sbjct: 175 KFTREEYVKLKAEG 188
>pdb|3IZS|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|I Chain I, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 221
Score = 272 bits (696), Expect = 3e-73, Method: Compositional matrix adjust.
Identities = 128/188 (68%), Positives = 149/188 (79%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSEALEA
Sbjct: 9 YRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSEALEAA 68
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADRLQ GMRGA+GKP G AR
Sbjct: 69 RICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKPHGLAAR 128
Query: 196 VNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 255
V+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT DR EY R+
Sbjct: 129 VDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAG 188
Query: 256 RILHDAHF 263
+ D F
Sbjct: 189 EVKDDGAF 196
Score = 173 bits (439), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 84/121 (69%), Positives = 97/121 (80%), Gaps = 2/121 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSEALEA
Sbjct: 9 YRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSEALEAA 68
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKYRAEHGPLA 468
RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADR + G + HG LA
Sbjct: 69 RICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQ-QGMRGAWGKPHG-LA 126
Query: 469 A 469
A
Sbjct: 127 A 127
Score = 103 bits (256), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 52/86 (60%), Positives = 62/86 (72%), Gaps = 4/86 (4%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQ GMRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA
Sbjct: 100 NKMLSCAGAD----RLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRA 155
Query: 315 KFKFPGRQKIYVSKKWGFTKYDREEY 340
++KFPG+QKI +SKKWGFT DR EY
Sbjct: 156 RYKFPGQQKIILSKKWGFTNLDRPEY 181
Score = 95.1 bits (235), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 44/67 (65%), Positives = 52/67 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT
Sbjct: 115 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFT 174
Query: 61 KYDREEY 67
DR EY
Sbjct: 175 NLDRPEY 181
>pdb|3J0L|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0Q|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
Length = 219
Score = 272 bits (695), Expect = 4e-73, Method: Compositional matrix adjust.
Identities = 128/188 (68%), Positives = 149/188 (79%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSEALEA
Sbjct: 7 YRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSEALEAA 66
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADRLQ GMRGA+GKP G AR
Sbjct: 67 RICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKPHGLAAR 126
Query: 196 VNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 255
V+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT DR EY R+
Sbjct: 127 VDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAG 186
Query: 256 RILHDAHF 263
+ D F
Sbjct: 187 EVKDDGAF 194
Score = 173 bits (438), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 84/121 (69%), Positives = 97/121 (80%), Gaps = 2/121 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSEALEA
Sbjct: 7 YRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSEALEAA 66
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKYRAEHGPLA 468
RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADR + G + HG LA
Sbjct: 67 RICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQ-QGMRGAWGKPHG-LA 124
Query: 469 A 469
A
Sbjct: 125 A 125
Score = 103 bits (256), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 52/86 (60%), Positives = 62/86 (72%), Gaps = 4/86 (4%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQ GMRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA
Sbjct: 98 NKMLSCAGAD----RLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRA 153
Query: 315 KFKFPGRQKIYVSKKWGFTKYDREEY 340
++KFPG+QKI +SKKWGFT DR EY
Sbjct: 154 RYKFPGQQKIILSKKWGFTNLDRPEY 179
Score = 95.1 bits (235), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 44/67 (65%), Positives = 52/67 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT
Sbjct: 113 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFT 172
Query: 61 KYDREEY 67
DR EY
Sbjct: 173 NLDRPEY 179
>pdb|3ZF7|K Chain K, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 213
Score = 270 bits (690), Expect = 1e-72, Method: Compositional matrix adjust.
Identities = 128/193 (66%), Positives = 152/193 (78%), Gaps = 4/193 (2%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YR+CKNKPYPKSRFCRGVPDP+IR FD+GK++A V++FP+CVH+VS E EQ+SSE
Sbjct: 4 RPARCYRFCKNKPYPKSRFCRGVPDPRIRTFDIGKRRAPVDEFPVCVHVVSRELEQISSE 63
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RI NKY+VK K+ FH+R+R HPFHV+RINKMLSCAGADRLQTGMR +YGKP
Sbjct: 64 ALEAARIQANKYMVKRANKECFHMRIRAHPFHVLRINKMLSCAGADRLQTGMRQSYGKPN 123
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYET 250
GT ARV IGQ ++S+R+ D + P +E+LRRAK KFPGRQ I +SK WGFT R EYE
Sbjct: 124 GTCARVRIGQILLSMRTKDTYVPQALESLRRAKMKFPGRQIIVISKYWGFTNILRNEYEE 183
Query: 251 LRD----QNRILH 259
LRD Q R LH
Sbjct: 184 LRDAGKLQQRGLH 196
Score = 171 bits (433), Expect = 8e-43, Method: Compositional matrix adjust.
Identities = 76/109 (69%), Positives = 92/109 (84%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YR+CKNKPYPKSRFCRGVPDP+IR FD+GK++A V++FP+CVH+VS E EQ+SSE
Sbjct: 4 RPARCYRFCKNKPYPKSRFCRGVPDPRIRTFDIGKRRAPVDEFPVCVHVVSRELEQISSE 63
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RI NKY+VK K+ FH+R+R HPFHV+RINKMLSCAGADR +
Sbjct: 64 ALEAARIQANKYMVKRANKECFHMRIRAHPFHVLRINKMLSCAGADRLQ 112
Score = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 53/91 (58%), Positives = 64/91 (70%), Gaps = 4/91 (4%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQTGMR +YGKP GT ARV IGQ ++S+R+ D + P +E+LRRA
Sbjct: 100 NKMLSCAGAD----RLQTGMRQSYGKPNGTCARVRIGQILLSMRTKDTYVPQALESLRRA 155
Query: 315 KFKFPGRQKIYVSKKWGFTKYDREEYETLRD 345
K KFPGRQ I +SK WGFT R EYE LRD
Sbjct: 156 KMKFPGRQIIVISKYWGFTNILRNEYEELRD 186
Score = 95.1 bits (235), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 44/72 (61%), Positives = 53/72 (73%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MR +YGKP GT ARV IGQ ++S+R+ D + P +E+LRRAK KFPGRQ I +SK WGFT
Sbjct: 115 MRQSYGKPNGTCARVRIGQILLSMRTKDTYVPQALESLRRAKMKFPGRQIIVISKYWGFT 174
Query: 61 KYDREEYETLRD 72
R EYE LRD
Sbjct: 175 NILRNEYEELRD 186
>pdb|2PA2|A Chain A, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
pdb|2PA2|B Chain B, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
Length = 151
Score = 258 bits (659), Expect = 5e-69, Method: Compositional matrix adjust.
Identities = 120/149 (80%), Positives = 138/149 (92%)
Query: 101 FDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHP 160
FDLG+KKAKV++FPLC H+VSDEYEQLSSEALEA RIC NKY+VK+CGKD FHIR+RLHP
Sbjct: 3 FDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHP 62
Query: 161 FHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALR 220
FHVIRINKMLSCAGADRLQTGMRGA+GKPQGTVARV+IGQ IMS+R+ + K VIEALR
Sbjct: 63 FHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALR 122
Query: 221 RAKFKFPGRQKIYVSKKWGFTKYDREEYE 249
RAKFKFPGRQKI++SKKWGFTK++ +E+E
Sbjct: 123 RAKFKFPGRQKIHISKKWGFTKFNADEFE 151
Score = 147 bits (370), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 66/79 (83%), Positives = 74/79 (93%)
Query: 374 FDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHP 433
FDLG+KKAKV++FPLC H+VSDEYEQLSSEALEA RIC NKY+VK+CGKD FHIR+RLHP
Sbjct: 3 FDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARICANKYMVKSCGKDGFHIRVRLHP 62
Query: 434 FHVIRINKMLSCAGADRFE 452
FHVIRINKMLSCAGADR +
Sbjct: 63 FHVIRINKMLSCAGADRLQ 81
Score = 119 bits (297), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 59/87 (67%), Positives = 72/87 (82%), Gaps = 4/87 (4%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQTGMRGA+GKPQGTVARV+IGQ IMS+R+ + K VIEALRRA
Sbjct: 69 NKMLSCAGAD----RLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRA 124
Query: 315 KFKFPGRQKIYVSKKWGFTKYDREEYE 341
KFKFPGRQKI++SKKWGFTK++ +E+E
Sbjct: 125 KFKFPGRQKIHISKKWGFTKFNADEFE 151
Score = 108 bits (270), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 50/68 (73%), Positives = 61/68 (89%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGTVARV+IGQ IMS+R+ + K VIEALRRAKFKFPGRQKI++SKKWGFT
Sbjct: 84 MRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFT 143
Query: 61 KYDREEYE 68
K++ +E+E
Sbjct: 144 KFNADEFE 151
>pdb|1S1I|I Chain I, 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 = 168
Score = 246 bits (627), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 116/165 (70%), Positives = 135/165 (81%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSE
Sbjct: 4 RPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSE 63
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADRLQ GMRGA+GKP
Sbjct: 64 ALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKPH 123
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 235
G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 124 GLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 168
Score = 173 bits (438), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 79/109 (72%), Positives = 91/109 (83%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSE
Sbjct: 4 RPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSE 63
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADR +
Sbjct: 64 ALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQ 112
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/73 (57%), Positives = 52/73 (71%), Gaps = 4/73 (5%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQ GMRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA
Sbjct: 100 NKMLSCAGAD----RLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRA 155
Query: 315 KFKFPGRQKIYVS 327
++KFPG+QKI +S
Sbjct: 156 RYKFPGQQKIILS 168
Score = 72.8 bits (177), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 34/54 (62%), Positives = 42/54 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 54
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 115 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 168
>pdb|3JYW|I Chain I, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 165
Score = 245 bits (626), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 116/165 (70%), Positives = 135/165 (81%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSE
Sbjct: 1 RPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSE 60
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADRLQ GMRGA+GKP
Sbjct: 61 ALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKPH 120
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 235
G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 121 GLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 165
Score = 172 bits (437), Expect = 3e-43, Method: Compositional matrix adjust.
Identities = 79/109 (72%), Positives = 91/109 (83%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YRY KNKPYPKSR+ R VPD KIRI+DLGKKKA V++FPLCVHLVS+E EQLSSE
Sbjct: 1 RPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSSE 60
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RIC NKY+ G+D FH+R+R+HPFHV+RINKMLSCAGADR +
Sbjct: 61 ALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQ 109
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/73 (57%), Positives = 52/73 (71%), Gaps = 4/73 (5%)
Query: 255 NRILHDAHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
N++L A D RLQ GMRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA
Sbjct: 97 NKMLSCAGAD----RLQQGMRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRA 152
Query: 315 KFKFPGRQKIYVS 327
++KFPG+QKI +S
Sbjct: 153 RYKFPGQQKIILS 165
Score = 72.8 bits (177), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 34/54 (62%), Positives = 42/54 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 54
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 112 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 165
>pdb|4A17|H Chain H, 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|H Chain H, 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|H Chain H, 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|H Chain H, 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 = 215
Score = 239 bits (609), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 115/191 (60%), Positives = 141/191 (73%)
Query: 71 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 130
R YR K KPYPKSR+ RGVPD +IRI+D G+KKA VE+FP VH+VSDE EQ++SE
Sbjct: 4 RPARCYRQPKGKPYPKSRYNRGVPDARIRIYDSGRKKATVEEFPYVVHIVSDEKEQITSE 63
Query: 131 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQ 190
ALEA RI NK L+K KD FH+R R+HP+HV+RINKMLSCAGADRLQ+GMRGA+GK
Sbjct: 64 ALEAARIAANKNLIKFISKDAFHLRCRVHPWHVLRINKMLSCAGADRLQSGMRGAFGKAL 123
Query: 191 GTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYET 250
G ARV+IG + SVR + I+AL RAK KFPGRQK+ S+KWGFTK R +Y
Sbjct: 124 GKAARVDIGSILFSVRVKEPHVKYAIDALTRAKAKFPGRQKVVTSQKWGFTKLTRAQYSR 183
Query: 251 LRDQNRILHDA 261
LR+Q +++ D
Sbjct: 184 LRNQKKLVTDG 194
Score = 153 bits (386), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 71/109 (65%), Positives = 85/109 (77%)
Query: 344 RDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSE 403
R YR K KPYPKSR+ RGVPD +IRI+D G+KKA VE+FP VH+VSDE EQ++SE
Sbjct: 4 RPARCYRQPKGKPYPKSRYNRGVPDARIRIYDSGRKKATVEEFPYVVHIVSDEKEQITSE 63
Query: 404 ALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
ALEA RI NK L+K KD FH+R R+HP+HV+RINKMLSCAGADR +
Sbjct: 64 ALEAARIAANKNLIKFISKDAFHLRCRVHPWHVLRINKMLSCAGADRLQ 112
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 58/139 (41%), Positives = 77/139 (55%), Gaps = 5/139 (3%)
Query: 208 SDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRILHDAHFDHWI 267
SD+ + EAL A+ ++SK + + LR N++L A D
Sbjct: 54 SDEKEQITSEALEAARIAANKNLIKFISKDAFHLRCRVHPWHVLRI-NKMLSCAGAD--- 109
Query: 268 IRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 327
RLQ+GMRGA+GK G ARV+IG + SVR + I+AL RAK KFPGRQK+ S
Sbjct: 110 -RLQSGMRGAFGKALGKAARVDIGSILFSVRVKEPHVKYAIDALTRAKAKFPGRQKVVTS 168
Query: 328 KKWGFTKYDREEYETLRDQ 346
+KWGFTK R +Y LR+Q
Sbjct: 169 QKWGFTKLTRAQYSRLRNQ 187
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 40/73 (54%), Positives = 49/73 (67%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GK G ARV+IG + SVR + I+AL RAK KFPGRQK+ S+KWGFT
Sbjct: 115 MRGAFGKALGKAARVDIGSILFSVRVKEPHVKYAIDALTRAKAKFPGRQKVVTSQKWGFT 174
Query: 61 KYDREEYETLRDQ 73
K R +Y LR+Q
Sbjct: 175 KLTRAQYSRLRNQ 187
>pdb|3J21|N Chain N, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 181
Score = 115 bits (287), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 64/159 (40%), Positives = 84/159 (52%), Gaps = 3/159 (1%)
Query: 69 TLRDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLS 128
LR RY Y + + RG P PKI IFD+G DF V L + E Q+
Sbjct: 2 ALRPAKIDRYVDKPAYTRREYIRGAPGPKITIFDMGNPAG---DFEFEVSLHTAEPVQIR 58
Query: 129 SEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGK 188
ALEA R N+YL KN G+ +H ++R++PF V+R N M + ADR GMR +GK
Sbjct: 59 QNALEAARQQVNRYLQKNVGRSNYHFKIRVYPFQVLRENPMATGRKADRYGNGMRRPFGK 118
Query: 189 PQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFP 227
P G AR+ Q I+S+R + + IE RRA KFP
Sbjct: 119 PIGLAARLKKDQKILSIRVNRQHLKFAIEGARRAAMKFP 157
Score = 81.6 bits (200), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 50/137 (36%), Positives = 69/137 (50%), Gaps = 4/137 (2%)
Query: 342 TLRDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLS 401
LR RY Y + + RG P PKI IFD+G DF V L + E Q+
Sbjct: 2 ALRPAKIDRYVDKPAYTRREYIRGAPGPKITIFDMGNPAG---DFEFEVSLHTAEPVQIR 58
Query: 402 SEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKYR 461
ALEA R N+YL KN G+ +H ++R++PF V+R N M + ADR+ +G +
Sbjct: 59 QNALEAARQQVNRYLQKNVGRSNYHFKIRVYPFQVLRENPMATGRKADRYG-NGMRRPFG 117
Query: 462 AEHGPLAAWKKVQEELA 478
G A KK Q+ L+
Sbjct: 118 KPIGLAARLKKDQKILS 134
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 28/51 (54%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFP 319
R GMR +GKP G AR+ Q I+S+R + + IE RRA KFP
Sbjct: 107 RYGNGMRRPFGKPIGLAARLKKDQKILSIRVNRQHLKFAIEGARRAAMKFP 157
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFP 46
MR +GKP G AR+ Q I+S+R + + IE RRA KFP
Sbjct: 112 MRRPFGKPIGLAARLKKDQKILSIRVNRQHLKFAIEGARRAAMKFP 157
>pdb|3I55|H Chain H, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|H Chain H, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 174
Score = 100 bits (249), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 55/162 (33%), Positives = 88/162 (54%), Gaps = 1/162 (0%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 136 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVA 194
R+ N++L+K G++ + + +R P V+R NK + AGADR+ GMR A+GK GT A
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAA 128
Query: 195 RVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 236
RV G+ + + + + V EA RRA K +I V +
Sbjct: 129 RVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
Score = 71.6 bits (174), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 36/113 (31%), Positives = 61/113 (53%), Gaps = 2/113 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 409 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKY 460
R+ N++L+K G++ + + +R P V+R NK + AGADR DG +
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVS-DGMRAAF 120
Score = 35.8 bits (81), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 328
R+ GMR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 111 RVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 55
MR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
>pdb|1YHQ|H Chain H, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|H Chain H, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|H Chain H, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|H Chain H, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|H Chain H, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|H Chain H, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|H Chain H, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CC2|H Chain H, 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|H Chain H, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|H Chain H, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|H Chain H, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|H Chain H, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|H Chain H, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|H Chain H, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|H Chain H, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|H Chain H, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|4ADX|H Chain H, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 177
Score = 100 bits (248), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 55/162 (33%), Positives = 88/162 (54%), Gaps = 1/162 (0%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 136 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVA 194
R+ N++L+K G++ + + +R P V+R NK + AGADR+ GMR A+GK GT A
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAA 128
Query: 195 RVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 236
RV G+ + + + + V EA RRA K +I V +
Sbjct: 129 RVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 36/113 (31%), Positives = 61/113 (53%), Gaps = 2/113 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 409 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKY 460
R+ N++L+K G++ + + +R P V+R NK + AGADR DG +
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVS-DGMRAAF 120
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 328
R+ GMR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 111 RVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 55
MR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
>pdb|1S72|H Chain H, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1VQ4|H Chain H, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|H Chain H, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|H Chain H, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|H Chain H, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|H Chain H, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|H Chain H, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|H Chain H, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|H Chain H, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|H Chain H, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|H Chain H, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|H Chain H, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|H Chain H, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|H Chain H, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|H Chain H, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|H Chain H, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
Length = 171
Score = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 52/148 (35%), Positives = 83/148 (56%), Gaps = 1/148 (0%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 6 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 65
Query: 136 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVA 194
R+ N++L+K G++ + + +R P V+R NK + AGADR+ GMR A+GK GT A
Sbjct: 66 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAA 125
Query: 195 RVNIGQPIMSVRSSDKFKPAVIEALRRA 222
RV G+ + + + + V EA RRA
Sbjct: 126 RVQAGEQLFTAYCNVEDAEHVKEAFRRA 153
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 36/113 (31%), Positives = 61/113 (53%), Gaps = 2/113 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 6 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 65
Query: 409 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKY 460
R+ N++L+K G++ + + +R P V+R NK + AGADR DG +
Sbjct: 66 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVS-DGMRAAF 117
Score = 35.0 bits (79), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 26/46 (56%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
R+ GMR A+GK GT ARV G+ + + + + V EA RRA
Sbjct: 108 RVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRA 153
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 41
MR A+GK GT ARV G+ + + + + V EA RRA
Sbjct: 113 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRA 153
>pdb|2QEX|H Chain H, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 174
Score = 99.8 bits (247), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 52/148 (35%), Positives = 83/148 (56%), Gaps = 1/148 (0%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 136 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVA 194
R+ N++L+K G++ + + +R P V+R NK + AGADR+ GMR A+GK GT A
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAA 128
Query: 195 RVNIGQPIMSVRSSDKFKPAVIEALRRA 222
RV G+ + + + + V EA RRA
Sbjct: 129 RVQAGEQLFTAYCNVEDAEHVKEAFRRA 156
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 36/113 (31%), Positives = 61/113 (53%), Gaps = 2/113 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR Y + + G+P KI +G+K+ +D+P+ + L+ +E QL +LEA
Sbjct: 9 YRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEAS 68
Query: 409 RICCNKYLVKNCGKD-QFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKY 460
R+ N++L+K G++ + + +R P V+R NK + AGADR DG +
Sbjct: 69 RLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVS-DGMRAAF 120
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 26/46 (56%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 314
R+ GMR A+GK GT ARV G+ + + + + V EA RRA
Sbjct: 111 RVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRA 156
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRA 41
MR A+GK GT ARV G+ + + + + V EA RRA
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRA 156
>pdb|1JJ2|H Chain H, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|H Chain H, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|J Chain J, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|J Chain J, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|J Chain J, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|J Chain J, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|J Chain J, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|J Chain J, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|J Chain J, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|J Chain J, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|J Chain J, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|J Chain J, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|J Chain J, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|J Chain J, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|J Chain J, 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|H Chain H, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|H Chain H, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|H Chain H, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|H Chain H, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|H Chain H, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 167
Score = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 56/150 (37%), Positives = 74/150 (49%), Gaps = 3/150 (2%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR Y + + G+P KI FD+G A +P V LV ++ Q+ ALEA
Sbjct: 6 YRNSSKPAYTRREYISGIPGKKIAQFDMGNNGAG-PTYPAQVELVVEKPVQIRHNALEAA 64
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
R+ N+Y+ + + R+R PFHVIR NK + A A GMR +GKP GT AR
Sbjct: 65 RVAANRYVQNSGAAANYKFRIRKFPFHVIRENKAAAAAAAAAAADGMRAPFGKPVGTAAR 124
Query: 196 VNIGQPIMSVRSSDKFKPAVIEALRRAKFK 225
V+ I + P V EA RRAK K
Sbjct: 125 VHGANHIFIAWVNP--DPNVEEAWRRAKMK 152
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/93 (35%), Positives = 47/93 (50%), Gaps = 1/93 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR Y + + G+P KI FD+G A +P V LV ++ Q+ ALEA
Sbjct: 6 YRNSSKPAYTRREYISGIPGKKIAQFDMGNNGAG-PTYPAQVELVVEKPVQIRHNALEAA 64
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINK 441
R+ N+Y+ + + R+R PFHVIR NK
Sbjct: 65 RVAANRYVQNSGAAANYKFRIRKFPFHVIRENK 97
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 273 GMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFK 317
GMR +GKP GT ARV+ I + P V EA RRAK K
Sbjct: 110 GMRAPFGKPVGTAARVHGANHIFIAWVNP--DPNVEEAWRRAKMK 152
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFK 44
MR +GKP GT ARV+ I + P V EA RRAK K
Sbjct: 111 MRAPFGKPVGTAARVHGANHIFIAWVNP--DPNVEEAWRRAKMK 152
>pdb|1FFK|F Chain F, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 157
Score = 55.8 bits (133), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 44/151 (29%), Positives = 66/151 (43%), Gaps = 15/151 (9%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
+R Y + + G+P I F +G A +P V V ++ Q+ ALEA
Sbjct: 6 FRNSIKPAYTRREYISGIPGKGIAQFKMGNNGAG-PTYPAQVENVVEKPVQIRHNALEAA 64
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
R N+++ + + R+R PFHVIR ++ GMR +GK GT AR
Sbjct: 65 RNAANRFVQNSGAAANYKFRIRKFPFHVIR----------EQDGDGMRAPFGKSVGTAAR 114
Query: 196 VN-IGQPIMSVRSSDKFKPAVIEALRRAKFK 225
+ ++ + D PAV A RRA K
Sbjct: 115 SHGANHDFIAWVNPD---PAVEFAWRRAYMK 142
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
+R Y + + G+P I F +G A +P V V ++ Q+ ALEA
Sbjct: 6 FRNSIKPAYTRREYISGIPGKGIAQFKMGNNGAG-PTYPAQVENVVEKPVQIRHNALEAA 64
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIR 438
R N+++ + + R+R PFHVIR
Sbjct: 65 RNAANRFVQNSGAAANYKFRIRKFPFHVIR 94
>pdb|1GIY|P Chain P, 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|1ML5|PP Chain p, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|P Chain P, 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|Q Chain Q, 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|Q Chain Q, 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|Q Chain Q, 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
Length = 138
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 45/141 (31%), Positives = 64/141 (45%), Gaps = 24/141 (17%)
Query: 86 KSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVK 145
+ + G+P I F +G +P V V ++ Q+ ALEA R N++ V+
Sbjct: 6 RREYISGIPGKGIAQFKMGNNT-----YPAQVENVVEKPVQIRHNALEAARNAANRF-VQ 59
Query: 146 NCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVARVN-IGQPIMS 204
N GK R+R PFHVIR ++ GMR +GK GT AR + ++
Sbjct: 60 NSGK----FRIRKFPFHVIR----------EQDGDGMRAPFGKSVGTAARSHGANHDFIA 105
Query: 205 VRSSDKFKPAVIEALRRAKFK 225
+ D PAV A RRA K
Sbjct: 106 WVNPD---PAVEFAWRRAYMK 123
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 359 KSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVK 418
+ + G+P I F +G +P V V ++ Q+ ALEA R N++ V+
Sbjct: 6 RREYISGIPGKGIAQFKMGNNT-----YPAQVENVVEKPVQIRHNALEAARNAANRF-VQ 59
Query: 419 NCGKDQFHIRMRLHPFHVIR 438
N GK R+R PFHVIR
Sbjct: 60 NSGK----FRIRKFPFHVIR 75
>pdb|1OB0|A Chain A, Kinetic Stabilization Of Bacillus Licheniformis-Amylase
Through Introduction Of Hydrophobic Residues At The
Surface
Length = 483
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 203 MSVRSSDKFKPAVIEALRRA--KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRI 257
+ V +D+ + E L +A F FPGR Y KW + +D +++ R NRI
Sbjct: 118 VEVDPADRNRVISGEVLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRI 174
>pdb|3OM4|A Chain A, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|B Chain B, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|C Chain C, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|D Chain D, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
Length = 456
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 11/95 (11%)
Query: 186 YGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK--Y 243
YGK T A+VN+ QP + + K ++ + K F G KIY + + + Y
Sbjct: 168 YGKQTLTTAQVNMSQP-----NDNTLK---VDGVEDYKSIFDGDGKIYQTVQQFIDEGGY 219
Query: 244 DREEYETLRDQNRILHDAHFDHWIIRLQTGMRGAY 278
D + TLRD + I + H + + TG Y
Sbjct: 220 DTGDNHTLRDPHYIEDNGH-KYLVFEANTGTEDGY 253
>pdb|3OM5|A Chain A, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|B Chain B, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|C Chain C, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|D Chain D, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
Length = 456
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 11/95 (11%)
Query: 186 YGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK--Y 243
YGK T A+VN+ QP + + K ++ + K F G KIY + + + Y
Sbjct: 168 YGKQTLTTAQVNMSQP-----NDNTLK---VDGVEDYKSIFDGDGKIYQTVQQFIDEGGY 219
Query: 244 DREEYETLRDQNRILHDAHFDHWIIRLQTGMRGAY 278
D + TLRD + I + H + + TG Y
Sbjct: 220 DTGDAHTLRDPHYIEDNGH-KYLVFEANTGTEDGY 253
>pdb|2GJP|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase,
Crystallized With The Substrate Analogue Acarbose And
Maltose
pdb|2GJR|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase Without Any
Substrate Analogues
Length = 485
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 215 VIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRD-QNRI 257
IEA KF FPGR Y KW + +D +++ R QNRI
Sbjct: 136 TIEAW--TKFDFPGRGNTYSDFKWRWYHFDGVDWDQSRQFQNRI 177
>pdb|1W9X|A Chain A, Bacillus Halmapalus Alpha Amylase
Length = 481
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 215 VIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRD-QNRI 257
IEA KF FPGR Y KW + +D +++ R QNRI
Sbjct: 132 TIEAW--TKFDFPGRGNTYSDFKWRWYHFDGVDWDQSRQFQNRI 173
>pdb|1VJS|A Chain A, Structure Of Alpha-Amylase Precursor
Length = 483
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 203 MSVRSSDKFKPAVIEALRRA--KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRI 257
+ V +D+ + E L +A F FPGR Y KW + +D +++ R NRI
Sbjct: 118 VEVDPADRNRVISGEHLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRI 174
>pdb|1BLI|A Chain A, Bacillus Licheniformis Alpha-Amylase
Length = 483
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 203 MSVRSSDKFKPAVIEALRRA--KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRI 257
+ V +D+ + E L +A F FPGR Y KW + +D +++ R NRI
Sbjct: 118 VEVDPADRNRVISGEHLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRI 174
>pdb|1BPL|A Chain A, Glycosyltransferase
Length = 189
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 203 MSVRSSDKFKPAVIEALRRA--KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRI 257
+ V +D+ + E L +A F FPGR Y KW + +D +++ R NRI
Sbjct: 118 VEVDPADRNRVISGEHLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRI 174
>pdb|1HVX|A Chain A, Bacillus Stearothermophilus Alpha-Amylase
Length = 515
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 222 AKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRI 257
KF FPGR Y S KW + +D +++ R +RI
Sbjct: 140 TKFDFPGRGNTYSSFKWRWYHFDGVDWDESRKLSRI 175
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 41 AKFKFPGRQKIYVSKKWGFTKYDREEYETLR 71
KF FPGR Y S KW + +D +++ R
Sbjct: 140 TKFDFPGRGNTYSSFKWRWYHFDGVDWDESR 170
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 314 AKFKFPGRQKIYVSKKWGFTKYDREEYETLR 344
KF FPGR Y S KW + +D +++ R
Sbjct: 140 TKFDFPGRGNTYSSFKWRWYHFDGVDWDESR 170
>pdb|3OM7|C Chain C, Crystal Structure Of B. Megaterium Levansucrase Mutant
Y247w
pdb|3OM7|A Chain A, Crystal Structure Of B. Megaterium Levansucrase Mutant
Y247w
pdb|3OM7|B Chain B, Crystal Structure Of B. Megaterium Levansucrase Mutant
Y247w
pdb|3OM7|D Chain D, Crystal Structure Of B. Megaterium Levansucrase Mutant
Y247w
Length = 456
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 11/95 (11%)
Query: 186 YGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK--Y 243
YGK T A+VN+ QP + + K ++ + K F G KIY + + + +
Sbjct: 168 YGKQTLTTAQVNMSQP-----NDNTLK---VDGVEDYKSIFDGDGKIYQTVQQFIDEGGW 219
Query: 244 DREEYETLRDQNRILHDAHFDHWIIRLQTGMRGAY 278
D + TLRD + I + H + + TG Y
Sbjct: 220 DTGDNHTLRDPHYIEDNGH-KYLVFEANTGTEDGY 253
>pdb|1E3X|A Chain A, Native Structure Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.92a
pdb|1E3Z|A Chain A, Acarbose Complex Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.93a
pdb|1E40|A Chain A, TrisMALTOTRIOSE COMPLEX OF CHIMAERIC AMYLASE FROM B.
Amyloliquefaciens And B. Licheniformis At 2.2a
pdb|1E43|A Chain A, Native Structure Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.7a
Length = 483
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 224 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRIL 258
F+FPGR Y KW + +D +++ R +RI
Sbjct: 139 FRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIF 173
>pdb|3BH4|A Chain A, High Resolution Crystal Structure Of Bacillus
Amyloliquefaciens Alpha-Amylase
pdb|3BH4|B Chain B, High Resolution Crystal Structure Of Bacillus
Amyloliquefaciens Alpha-Amylase
Length = 483
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 224 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRIL 258
F+FPGR Y KW + +D +++ R +RI
Sbjct: 139 FRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIF 173
>pdb|3LKB|A Chain A, Crystal Structure Of A Branched Chain Amino Acid Abc
Transporter From Thermus Thermophilus With Bound Valine
pdb|3LKB|B Chain B, Crystal Structure Of A Branched Chain Amino Acid Abc
Transporter From Thermus Thermophilus With Bound Valine
Length = 392
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 261 AHFDHWIIRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKF 318
AH D IRLQ + YG+P+ + VN +++ + +EA+RRA+ +F
Sbjct: 258 AHEDTPGIRLQKEIGRKYGRPENFIESVNYTNGMLAAAIA-------VEAIRRAQERF 308
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
0.323 0.139 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,760,796
Number of Sequences: 62578
Number of extensions: 635825
Number of successful extensions: 1854
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1745
Number of HSP's gapped (non-prelim): 105
length of query: 480
length of database: 14,973,337
effective HSP length: 103
effective length of query: 377
effective length of database: 8,527,803
effective search space: 3214981731
effective search space used: 3214981731
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)