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= 020243
(329 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MI6|A Chain A, Docking Of The Modified Rf2 X-Ray Structure Into The Low
Resolution Cryo-Em Map Of Rf2 E.Coli 70s Ribosome
Length = 365
Score = 139 bits (349), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 95/325 (29%), Positives = 172/325 (52%), Gaps = 14/325 (4%)
Query: 6 NLWDDPTKSNEVLVKLADSLK-VVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRA 64
++W++P ++ + L K SL+ VV+ L ++ E+ + +LA +EA D F A A
Sbjct: 45 DVWNEPERA-QALGKERSSLEAVVDTLDQMKQGLEDVSGLLELA-VEADDEETFNEAV-A 101
Query: 65 SLD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGY 123
LD + + L Q E ++ G D + I+AGS G + WA L MY+RWA+ G+
Sbjct: 102 ELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGF 161
Query: 124 RGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACV 180
+ ++++ + G+KS TI+ +YA+G+L ETG H L+ F +G H + +
Sbjct: 162 KTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRH-TSFSSA 220
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERN 237
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI Q +R+
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRS 279
Query: 238 HFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKT 297
NK +A+ ++KAKL + ++ + ++ W + R YV + ++D++T
Sbjct: 280 QHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSR-IKDLRT 338
Query: 298 GIQLPDFNSVLDGNIKPFIEAHINS 322
G++ + +VLDG++ FIEA + +
Sbjct: 339 GVETRNTQAVLDGSLDQFIEASLKA 363
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 139 bits (349), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 95/325 (29%), Positives = 172/325 (52%), Gaps = 14/325 (4%)
Query: 6 NLWDDPTKSNEVLVKLADSLK-VVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRA 64
++W++P ++ + L K SL+ VV+ L ++ E+ + +LA +EA D F A A
Sbjct: 45 DVWNEPERA-QALGKERSSLEAVVDTLDQMKQGLEDVSGLLELA-VEADDEETFNEAV-A 101
Query: 65 SLD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGY 123
LD + + L Q E ++ G D + I+AGS G + WA L MY+RWA+ G+
Sbjct: 102 ELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGF 161
Query: 124 RGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACV 180
+ ++++ + G+KS TI+ +YA+G+L ETG H L+ F +G H + +
Sbjct: 162 KTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRH-TSFSSA 220
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERN 237
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI Q +R+
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRS 279
Query: 238 HFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKT 297
NK +A+ ++KAKL + ++ + ++ W + R YV + ++D++T
Sbjct: 280 QHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSR-IKDLRT 338
Query: 298 GIQLPDFNSVLDGNIKPFIEAHINS 322
G++ + +VLDG++ FIEA + +
Sbjct: 339 GVETRNTQAVLDGSLDQFIEASLKA 363
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 130 bits (326), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 94/325 (28%), Positives = 166/325 (51%), Gaps = 14/325 (4%)
Query: 6 NLWDDPTKSNEVLVKLADSLK-VVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRA 64
++W++P ++ + L K SL+ VV+ L + E+ + +LA +EA D F A A
Sbjct: 45 DVWNEPERA-QALGKERSSLEAVVDTLDQXKQGLEDVSGLLELA-VEADDEETFNEAV-A 101
Query: 65 SLD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGY 123
LD + + L Q E + G D + I+AGS G + WA L Y+RWA+ G+
Sbjct: 102 ELDALEEKLAQLEFRRXFSGEYDSADCYLDIQAGSGGTEAQDWASXLERXYLRWAESRGF 161
Query: 124 RGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACV 180
+ ++++ + G+KS TI+ +YA+G+L ETG H L+ F +G H + +
Sbjct: 162 KTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRH-TSFSSA 220
Query: 181 DVVPLFLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERN 237
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI Q +R+
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRS 279
Query: 238 HFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKT 297
NK +A + KAKL + ++ + + W + R YV + ++D++T
Sbjct: 280 QHKNKDQAXKQXKAKLYEVEXQKKNAEKQAXEDNKSDIGWGSQIRSYVLDDSR-IKDLRT 338
Query: 298 GIQLPDFNSVLDGNIKPFIEAHINS 322
G++ + +VLDG++ FIEA + +
Sbjct: 339 GVETRNTQAVLDGSLDQFIEASLKA 363
>pdb|2X9R|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|Y Chain Y, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
Length = 351
Score = 97.8 bits (242), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 88/321 (27%), Positives = 149/321 (46%), Gaps = 12/321 (3%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L +++ L+ + E+ A + + A +
Sbjct: 32 SLWNDPEAARKVSQEAARLRRTVDTFRSL--ESDLQGLLELMEELPAEE----REALKPE 85
Query: 66 LD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYR 124
L+ +K LD+ LL P+ + A +TI+ G+ G WAE LL MY R+A+++G++
Sbjct: 86 LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQ 145
Query: 125 GRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVD 181
VVD G+ A I + E A+G LS E G H L+ F H +
Sbjct: 146 VEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEV 205
Query: 182 VVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQSLGERNHFA 240
+ + E L+ + + S PG + + A + H+PTGI V R+
Sbjct: 206 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIK 265
Query: 241 NKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQ 300
NK AL LKA+L + ++ + ++ E W + R YV V+D +TG+
Sbjct: 266 NKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRTGLM 324
Query: 301 LPDFNSVLDGNIKPFIEAHIN 321
D +VLDG++ I A +
Sbjct: 325 RHDPENVLDGDLMDLIWAGLE 345
>pdb|2WH1|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|Y Chain Y, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit
Length = 351
Score = 97.8 bits (242), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 88/321 (27%), Positives = 149/321 (46%), Gaps = 12/321 (3%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L +++ L+ + E+ A + + A +
Sbjct: 32 SLWNDPEAARKVSQEAARLRRTVDTFRSL--ESDLQGLLELMEELPAEE----REALKPE 85
Query: 66 LD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYR 124
L+ +K LD+ LL P+ + A +TI+ G+ G WAE LL MY R+A+++G++
Sbjct: 86 LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQ 145
Query: 125 GRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVD 181
VVD G+ A I + E A+G LS E G H L+ F H +
Sbjct: 146 VEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEV 205
Query: 182 VVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQSLGERNHFA 240
+ + E L+ + + S PG + + A + H+PTGI V R+
Sbjct: 206 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIK 265
Query: 241 NKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQ 300
NK AL LKA+L + ++ + ++ E W + R YV V+D +TG+
Sbjct: 266 NKELALKILKARLYELERKKREEELKALRGEVEPIEWGSQIRSYVLD-KNYVKDHRTGLM 324
Query: 301 LPDFNSVLDGNIKPFIEAHIN 321
D +VLDG++ I A +
Sbjct: 325 RHDPENVLDGDLMDLIWAGLE 345
>pdb|2B9M|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400
Length = 365
Score = 97.4 bits (241), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 90/321 (28%), Positives = 146/321 (45%), Gaps = 12/321 (3%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L E+ L L ME + + A +
Sbjct: 37 SLWNDPEAARKVSQEAARLRRTVDTFRSL-----ESDLQGLLELMEELP-AEEREALKPE 90
Query: 66 LD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYR 124
L+ +K LD+ LL P+ + A +TI+ G+ G WAE LL MY R+A+++G++
Sbjct: 91 LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQ 150
Query: 125 GRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVD 181
VVD G+ A I + E A+G LS E G H L+ F H +
Sbjct: 151 VEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEV 210
Query: 182 VVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQSLGERNHFA 240
+ + E L+ + + S PG + + A + H+PTGI V R+
Sbjct: 211 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIK 270
Query: 241 NKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQ 300
NK AL LKA+L + ++ + ++ E W + R YV V+D +TG+
Sbjct: 271 NKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRTGLM 329
Query: 301 LPDFNSVLDGNIKPFIEAHIN 321
D +VLDG++ I A +
Sbjct: 330 RHDPENVLDGDLMDLIWAGLE 350
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 97.4 bits (241), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 88/321 (27%), Positives = 149/321 (46%), Gaps = 12/321 (3%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L +++ L+ + E+ A + + A +
Sbjct: 37 SLWNDPEAARKVSQEAARLRRTVDTFRSL--ESDLQGLLELMEELPAEE----REALKPE 90
Query: 66 LD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYR 124
L+ +K LD+ LL P+ + A +TI+ G+ G WAE LL MY R+A+++G++
Sbjct: 91 LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQ 150
Query: 125 GRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVD 181
VVD G+ A I + E A+G LS E G H L+ F H +
Sbjct: 151 VEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEV 210
Query: 182 VVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQSLGERNHFA 240
+ + E L+ + + S PG + + A + H+PTGI V R+
Sbjct: 211 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIK 270
Query: 241 NKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQ 300
NK AL LKA+L + ++ + ++ E W + R YV V+D +TG+
Sbjct: 271 NKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRTGLM 329
Query: 301 LPDFNSVLDGNIKPFIEAHIN 321
D +VLDG++ I A +
Sbjct: 330 RHDPENVLDGDLMDLIWAGLE 350
>pdb|3F1E|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|X Chain X, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400
Length = 378
Score = 97.4 bits (241), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 90/320 (28%), Positives = 146/320 (45%), Gaps = 12/320 (3%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L E+ L L ME + + A +
Sbjct: 50 SLWNDPEAARKVSQEAARLRRTVDTFRSL-----ESDLQGLLELMEELP-AEEREALKPE 103
Query: 66 LD-VSKLLDQYEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYR 124
L+ +K LD+ LL P+ + A +TI+ G+ G WAE LL MY R+A+++G++
Sbjct: 104 LEEAAKKLDELYHQTLLNFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQ 163
Query: 125 GRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLIN---FPNGSFPHEATLACVD 181
VVD G+ A I + E A+G LS E G H L+ F H +
Sbjct: 164 VEVVDLTPGPEAGIDYAQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEV 223
Query: 182 VVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQSLGERNHFA 240
+ + E L+ + + S PG + + A + H+PTGI V R+
Sbjct: 224 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIK 283
Query: 241 NKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQ 300
NK AL LKA+L + ++ + ++ E W + R YV V+D +TG+
Sbjct: 284 NKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLD-KNYVKDHRTGLM 342
Query: 301 LPDFNSVLDGNIKPFIEAHI 320
D +VLDG++ I A +
Sbjct: 343 RHDPENVLDGDLMDLIWAGL 362
>pdb|2FVO|A Chain A, Docking Of The Modified Rf1 X-ray Structure Into The Low
Resolution Cryo-em Map Of E.coli 70s Ribosome Bound With
Rf1
Length = 333
Score = 94.4 bits (233), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 74/254 (29%), Positives = 117/254 (46%), Gaps = 10/254 (3%)
Query: 70 KLLDQ-YEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVV 128
K LDQ Y+ L P + A V I+ G+ G ++A L MY R+A+++G+ V
Sbjct: 67 KELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVA 126
Query: 129 DKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP---NGSFPHEATLACVDVVPL 185
+ GG++ + + A+G L E+G H + P +G H +T A V V+P
Sbjct: 127 EIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTST-ATVAVLPE 185
Query: 186 FLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHFANK 242
E D++I EDL F + G+ + + A I H+PTGI V ER+ + NK
Sbjct: 186 IEE--KDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 243 MKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLP 302
AL L+A+L + EQ +S ++ I + E R + P V D +
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSY 303
Query: 303 DFNSVLDGNIKPFI 316
+LDG++ I
Sbjct: 304 RLQEILDGDLDEII 317
>pdb|1RQ0|A Chain A, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|B Chain B, Crystal Structure Of Peptide Releasing Factor 1
pdb|1RQ0|C Chain C, Crystal Structure Of Peptide Releasing Factor 1
Length = 342
Score = 94.4 bits (233), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 74/254 (29%), Positives = 117/254 (46%), Gaps = 10/254 (3%)
Query: 70 KLLDQ-YEMSKLLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVV 128
K LDQ Y+ L P + A V I+ G+ G ++A L MY R+A+++G+ V
Sbjct: 67 KELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVA 126
Query: 129 DKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP---NGSFPHEATLACVDVVPL 185
+ GG++ + + A+G L E+G H + P +G H +T A V V+P
Sbjct: 127 EIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTST-ATVAVLPE 185
Query: 186 FLETSPDLQISDEDL---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHFANK 242
E D++I EDL F + G+ + + A I H+PTGI V ER+ + NK
Sbjct: 186 IEE--KDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNK 243
Query: 243 MKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLP 302
AL L+A+L + EQ +S ++ I + E R + P V D +
Sbjct: 244 QTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSY 303
Query: 303 DFNSVLDGNIKPFI 316
+LDG++ I
Sbjct: 304 RLQEILDGDLDEII 317
>pdb|2B64|Y Chain Y, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|3D5A|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|X Chain X, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3MR8|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|V Chain V, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s)
Length = 354
Score = 88.2 bits (217), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 74/266 (27%), Positives = 117/266 (43%), Gaps = 9/266 (3%)
Query: 60 RAYRASLDVSKLLDQYEMSKLL--RGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRW 117
+A R +L K + E+ + L + P D A V I+AG+ G ++A L NMY+R+
Sbjct: 75 KAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEEAALFARDLFNMYLRF 134
Query: 118 ADKEGYRGRVVDKCCCKNGGVKSATIEFEFEYAFGYLSGETGAHCLINFP----NGSFPH 173
A++ G+ V+D GG E A+G E+G H + P G H
Sbjct: 135 AEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESGVHRVQRVPVTETQGRI-H 193
Query: 174 EATLACVDVVPLFLETSPDLQISDEDLLFSSPSLPGERQ-SIAKPAACIQHIPTGIAVQS 232
+T A V V+P E L + + + S PG + + A + H+PTGI V
Sbjct: 194 TST-ATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTC 252
Query: 233 LGERNHFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLV 292
R+ N+ KAL L+++LL + + + + I + E R + P V
Sbjct: 253 QDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNFPQSRV 312
Query: 293 QDVKTGIQLPDFNSVLDGNIKPFIEA 318
D + G D VL G++ P +EA
Sbjct: 313 TDHRIGFTTHDLEGVLSGHLTPILEA 338
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 64/246 (26%), Positives = 112/246 (45%), Gaps = 8/246 (3%)
Query: 82 RGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVKSA 141
+ P+D A + ++AG+ G ++A L MY R+A+ +R ++ ++GG K
Sbjct: 103 KDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEI 162
Query: 142 TIEFEFEYAFGYLSGETGAHCLINFP-NGSFPHEATLAC-VDVVPLFLETS-PDLQISDE 198
+ + +G L E+G H + P S T AC V V+P + PD+ +D
Sbjct: 163 IAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADL 222
Query: 199 DL-LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKLLVIV 257
+ F S G+ + A I H+PTGI V+ ER+ NK KAL+ L A++
Sbjct: 223 RIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAE 282
Query: 258 GEQGVSNVSCIKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLPDFNSVLDGN----IK 313
+ + +R + + + + R + P V D + + L + V++G I+
Sbjct: 283 MAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIE 342
Query: 314 PFIEAH 319
P I+ H
Sbjct: 343 PIIQEH 348
>pdb|1ZBT|A Chain A, Crystal Structure Of Peptide Chain Release Factor 1 (rf-1)
(smu.1085) From Streptococcus Mutans At 2.34 A
Resolution
Length = 371
Score = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 58/245 (23%), Positives = 105/245 (42%), Gaps = 5/245 (2%)
Query: 80 LLRGPNDVEGASVTIKAGSNGICPEIWAEQLLNMYVRWADKEGYRGRVVDKCCCKNGGVK 139
L + PND + + I+ + G ++A LLN Y ++A+ +G++ V + GG+K
Sbjct: 115 LPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNXYQKYAENQGWKFEVXEASANGVGGLK 174
Query: 140 SATIEFEFEYAFGYLSGETGAHCLINFPNGSFPHEATLACVDVVPLFLETSPDLQISDED 199
+ + L E+GAH + P + V+ + +I +D
Sbjct: 175 EVVAXVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVXPEVEEVEYEIDPKD 234
Query: 200 L---LFSSPSLPGERQSIAKPAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKLLVI 256
L ++ + G+ + A I H+PT I V+ ER N+ KA ++A++
Sbjct: 235 LRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEXQEERTQQKNRDKAXKIIRARVADH 294
Query: 257 VGEQGVSNVSCIKREAIVNIWQRETR-RYVSHPYKLVQDVKTGIQLPDFNSVLDGNIKPF 315
Q + +R++ V R R R + P V D + G+ L +S+L G +
Sbjct: 295 FA-QIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTDHRIGLTLQKLDSILSGKLDEV 353
Query: 316 IEAHI 320
I+A I
Sbjct: 354 IDALI 358
>pdb|3DC8|A Chain A, Crystal Structure Of Dihydropyrimidinase From
Sinorhizobium Meliloti
pdb|3DC8|B Chain B, Crystal Structure Of Dihydropyrimidinase From
Sinorhizobium Meliloti
Length = 490
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 12/83 (14%)
Query: 214 IAKPAACIQHIPTGIAVQSLGERNHFANKMKALNRLKAKLLVIVGEQGVSNVSCIKREAI 273
IA A C +I V + E+ H +A+ R +AK + + GE + +++ + E
Sbjct: 224 IADMAGCPVYI-----VHTSCEQAH-----EAIRRARAKGMRVFGEPLIQHLTLDETEYF 273
Query: 274 VNIWQRETRRYVSHPY--KLVQD 294
W RR +S P+ KL QD
Sbjct: 274 DKDWDHAARRVMSPPFRNKLHQD 296
>pdb|2DLA|A Chain A, Primase Large Subunit Amino Terminal Domain From
Pyrococcus Horikoshii
pdb|2DLA|B Chain B, Primase Large Subunit Amino Terminal Domain From
Pyrococcus Horikoshii
pdb|2DLA|C Chain C, Primase Large Subunit Amino Terminal Domain From
Pyrococcus Horikoshii
Length = 222
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 268 IKREAIVNIWQRETRRYVSHPYKLVQDVKTGIQLPDFNSVLDGNIKPFIEAHINSR 323
+KRE ++ IW + R V ++ +++ +LP+F + G I+ F E +
Sbjct: 164 LKREDLIRIWSKAFERNVERGVNMLYEIRD--ELPEFYRKVLGEIQAFAEEEFGRK 217
>pdb|3ZVR|A Chain A, Crystal Structure Of Dynamin
Length = 772
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 278 QRETRRYVSHPYKLVQDVKTGIQLPD--FNSVLDGNIKPFIEAHI 320
++E RR +S+ K + D++TG+ PD F + + ++ E I
Sbjct: 401 EKELRREISYAIKNIHDIRTGLFTPDLAFEATVKKQVQKLKEPSI 445
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 29 NALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
N +KD +KA+ + +AQLAE EA+ F A A+
Sbjct: 380 NFIKDAGFKAQISSWLAQLAEDEALRANTFAMATEAT 416
>pdb|3DM5|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus.
pdb|3DM5|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus
Length = 443
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 51 EAIDYGLFKRAYRAS----LDVSKLLDQY-EMSKLLRGPN 85
E I+Y KR R S DV +LLDQY +M KL + N
Sbjct: 391 EIINYSRIKRIARGSGTSTKDVKELLDQYRQMKKLFKSMN 430
>pdb|1PJB|A Chain A, L-alanine Dehydrogenase
pdb|1SAY|A Chain A, L-Alanine Dehydrogenase Complexed With Pyruvate
pdb|1PJC|A Chain A, L-Alanine Dehydrogenase Complexed With Nad
Length = 361
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 195 ISDEDLLFSSPSLPGERQSIAKPAACIQHIPTG 227
+++ DLL + +PG R I PA+ ++ + TG
Sbjct: 228 VAEADLLIGAVLVPGRRAPILVPASLVEQMRTG 260
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 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,744,373
Number of Sequences: 62578
Number of extensions: 404467
Number of successful extensions: 1025
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 979
Number of HSP's gapped (non-prelim): 23
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
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: 52 (24.6 bits)