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= 026460
(238 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ML5|Z Chain Z, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
Length = 365
Score = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 13/234 (5%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAVR 231
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI +
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQ 273
>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 = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 13/234 (5%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAVR 231
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI +
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQ 273
>pdb|1GQE|A Chain A, Polypeptide Chain Release Factor 2 (Rf2) From Escherichia
Coli
Length = 365
Score = 94.4 bits (233), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 70/234 (29%), Positives = 120/234 (51%), Gaps = 13/234 (5%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAVR 231
V P ++ D++I+ DL ++ + G+ + + A I HIPTGI +
Sbjct: 221 FVYPE-VDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQ 273
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 65/230 (28%), Positives = 105/230 (45%), Gaps = 11/230 (4%)
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 VVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+ + E L+ + + S P G+ + A + H+PTGI V
Sbjct: 211 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 260
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 63/230 (27%), Positives = 108/230 (46%), Gaps = 11/230 (4%)
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 VVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+ + E L+ + + S P G+ + A + H+PTGI V
Sbjct: 206 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 255
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 65/230 (28%), Positives = 105/230 (45%), Gaps = 11/230 (4%)
Query: 6 NLWDDPTKSNEVLVKLADSLKVVNALKDLRYKAEEAKLIAQLAEMEAIDYGLFKRAYRAS 65
+LW+DP + +V + A + V+ + L E+ L L ME + + A +
Sbjct: 32 SLWNDPEAARKVSQEAARLRRTVDTFRSL-----ESDLQGLLELMEELP-AEEREALKPE 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 VVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+ + E L+ + + S P G+ + A + H+PTGI V
Sbjct: 206 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 255
>pdb|2IHR|1 Chain 1, Rf2 Of Thermus Thermophilus
Length = 365
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 65/230 (28%), Positives = 105/230 (45%), Gaps = 11/230 (4%)
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 VVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+ + E L+ + + S P G+ + A + H+PTGI V
Sbjct: 211 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 260
>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 = 72.4 bits (176), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 65/230 (28%), Positives = 105/230 (45%), Gaps = 11/230 (4%)
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 VVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+ + E L+ + + S P G+ + A + H+PTGI V
Sbjct: 224 IPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 273
>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 = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 52/168 (30%), Positives = 81/168 (48%), Gaps = 10/168 (5%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAV 230
E D++I EDL F + G+ + + A I H+PTGI V
Sbjct: 186 IEE--KDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVV 231
>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 = 67.4 bits (163), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 52/168 (30%), Positives = 81/168 (48%), Gaps = 10/168 (5%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAV 230
E D++I EDL F + G+ + + A I H+PTGI V
Sbjct: 186 IEE--KDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVV 231
>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 = 60.8 bits (146), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 52/178 (29%), Positives = 80/178 (44%), Gaps = 9/178 (5%)
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 EATLACVDVVPLFLETSPDLQISDEDLLFSSPSLP-GERQSIAKPAACIQHIPTGIAV 230
+T A V V+P E L + + + S P G+ + A + H+PTGI V
Sbjct: 194 TST-ATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMV 250
>pdb|2B3T|B Chain B, Molecular Basis For Bacterial Class 1 Release Factor
Methylation By Prmc
Length = 360
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 43/153 (28%), Positives = 71/153 (46%), Gaps = 4/153 (2%)
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-LFSSPSLPGERQSIAKPAACIQHIPTGIAV 230
+ F S G+ + A I H+PTGI V
Sbjct: 223 RIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVV 255
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 35/154 (22%), Positives = 65/154 (42%), Gaps = 3/154 (1%)
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---LFSSPSLPGERQSIAKPAACIQHIPTGIAV 230
L ++ + G+ + A I H+PT I V
Sbjct: 235 LRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKV 268
>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 = 28.5 bits (62), Expect = 3.1, 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|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A
Novel E3 Ligase
Length = 622
Score = 28.1 bits (61), Expect = 3.9, 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|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 = 5.7, 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 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,185,916
Number of Sequences: 62578
Number of extensions: 300964
Number of successful extensions: 782
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 749
Number of HSP's gapped (non-prelim): 23
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)