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= 001573
(1051 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4I99|A Chain A, Crystal Structure Of The Smchead Bound To The C-winged
Helix Domain Of Scpa
pdb|4I99|B Chain B, Crystal Structure Of The Smchead Bound To The C-winged
Helix Domain Of Scpa
Length = 354
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 40/153 (26%), Positives = 75/153 (49%), Gaps = 14/153 (9%)
Query: 25 EIELHNFMTFDHL-ICKPGSR-LNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSIGA 82
++EL F ++ + + P S+ ++G NGSGKS++ AI LGG + RA+ I
Sbjct: 6 KLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASRISD 65
Query: 83 YVKRGEE----SGYIKISL------RG-DTKEEHLTIMRKIDTRNKSEWFFNGKVVPKGE 131
+ G + + Y ++++ RG E+ + I R++ +S ++ NG+ + E
Sbjct: 66 LIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATRSE 125
Query: 132 VLEITKRFNIQVNNLTQFLPQDRVCEFAKLSPV 164
+L+I I + L D + +F K SP+
Sbjct: 126 ILDILTAAXISPDGYNIVLQGD-ITKFIKXSPL 157
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/141 (24%), Positives = 73/141 (51%), Gaps = 12/141 (8%)
Query: 884 NLVAQINETFSRNFQE----MAVAGEVSLDEHESDFDKFGILIKVKFRQSGQLEVLSAHH 939
N+ + E SRNF E ++ G L E+ D F ++++ + +G+ +V
Sbjct: 188 NVFXRTFEAISRNFSEIFAKLSPGGSARL-ILENPEDPFSGGLEIEAKPAGK-DVKRIEA 245
Query: 940 QSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAASQPNTPQCF 999
SGGE++++ + ++ ++Q PF + DEI+ +D N +++ L++ +S+ + Q
Sbjct: 246 XSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRV-ADLIKESSKES--QFI 302
Query: 1000 LLTPKLLPDLEYSEACSILNI 1020
++T L D+ + A I+ +
Sbjct: 303 VIT---LRDVXXANADKIIGV 320
>pdb|1XEW|X Chain X, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases.
pdb|1XEX|A Chain A, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 182
Score = 48.5 bits (114), Expect = 2e-05, Method: Composition-based stats.
Identities = 41/156 (26%), Positives = 78/156 (50%), Gaps = 14/156 (8%)
Query: 23 IIEIELHNFMTF-DHLICKPGSR-LNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSI 80
I ++EL F ++ + + P S+ ++G NGSGKS++ AI LGG + RA+ I
Sbjct: 4 IEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRASRI 63
Query: 81 GAYVKRGEE----SGYIKISL------RG-DTKEEHLTIMRKIDTRNKSEWFFNGKVVPK 129
+ G + + Y ++++ RG E+ + I R++ +S ++ NG+ +
Sbjct: 64 SDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATR 123
Query: 130 GEVLEITKRFNIQVNNLTQFLPQDRVCEFAKLSPVK 165
E+L+I I + L D + +F K+SP++
Sbjct: 124 SEILDILTAAMISPDGYNIVLQGD-ITKFIKMSPLE 158
>pdb|3KTA|A Chain A, Structural Basis For Adenylate Kinase Activity In Abc
Atpases
pdb|3KTA|C Chain C, Structural Basis For Adenylate Kinase Activity In Abc
Atpases
Length = 182
Score = 47.8 bits (112), Expect = 3e-05, Method: Composition-based stats.
Identities = 41/156 (26%), Positives = 77/156 (49%), Gaps = 14/156 (8%)
Query: 23 IIEIELHNFMTF-DHLICKPGSR-LNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSI 80
I ++EL F ++ + + P S+ ++G NGSGKS++ AI LGG + RA+ I
Sbjct: 4 IEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASRI 63
Query: 81 GAYVKRGEE----SGYIKISL------RG-DTKEEHLTIMRKIDTRNKSEWFFNGKVVPK 129
+ G + + Y ++++ RG E+ + I R++ +S ++ NG+ +
Sbjct: 64 SDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATR 123
Query: 130 GEVLEITKRFNIQVNNLTQFLPQDRVCEFAKLSPVK 165
E+L+I I + L D + +F K SP++
Sbjct: 124 SEILDILTAAXISPDGYNIVLQGD-ITKFIKXSPLE 158
>pdb|3AUX|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|A Chain A, Crystal Structure Of Rad50 Bound To Adp
pdb|3AUY|B Chain B, Crystal Structure Of Rad50 Bound To Adp
pdb|3AV0|B Chain B, Crystal Structure Of Mre11-Rad50 Bound To Atp S
Length = 371
Score = 47.0 bits (110), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 60/228 (26%), Positives = 113/228 (49%), Gaps = 32/228 (14%)
Query: 25 EIELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSIGAYV 84
EI ++NF + + K + +IG NGSGKSS+ A+ AL G G + +
Sbjct: 7 EIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGA----GSNFNYDTII 62
Query: 85 KRGEESGYIKISLRGDTKEEHLTIMRKIDT-RNKSEWFFNGK-------VVPKG--EVLE 134
+G++S Y+++ + + I+R+ D+ R ++ + NGK V K E+L
Sbjct: 63 TKGKKSVYVELDF--EVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILG 120
Query: 135 ITKRFNIQVNNLTQFLPQDRVCEFAKLSPVKLLEETEKAVGDPQLPVQHC------ALVE 188
+ + N+ +N++ ++ Q + +F L P + LE K +G + + C + E
Sbjct: 121 VDR--NMFLNSI--YIKQGEIAKFLSLKPSEKLETVAKLLGIDEF--EKCYQKMGEIVKE 174
Query: 189 KSSKLKTIECTVKRNGDTLN-QLKAL-NVEQEKDVERVRQRAELLEKV 234
+L+ IE + ++L +LK + N+E+EK E++ + E L+KV
Sbjct: 175 YEKRLERIEGELNYKEESLKARLKEMSNLEKEK--EKLTKFVEYLDKV 220
>pdb|1W1W|A Chain A, Sc Smc1hd:scc1-c Complex, Atpgs
pdb|1W1W|B Chain B, Sc Smc1hd:scc1-c Complex, Atpgs
pdb|1W1W|C Chain C, Sc Smc1hd:scc1-c Complex, Atpgs
pdb|1W1W|D Chain D, Sc Smc1hd:scc1-c Complex, Atpgs
Length = 430
Score = 46.2 bits (108), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 77/180 (42%), Gaps = 26/180 (14%)
Query: 21 GNIIEIELHNFMTFDHLICKPG---SRLNLVIGPNGSGKSSLVCAIALALGGDTQLLGRA 77
G ++ +EL NF ++ + K G S +IGPNGSGKS+++ AI+ LG + L R+
Sbjct: 2 GRLVGLELSNFKSY-RGVTKVGFGESNFTSIIGPNGSGKSNMMDAISFVLGVRSNHL-RS 59
Query: 78 TSIGAYVKRG-------------------EESGYIKISLRGDTKEEHLTIMRKIDTRNKS 118
+ + RG +S Y+K + K + +MR I +
Sbjct: 60 NILKDLIYRGVLNDENSDDYDNEGAASSNPQSAYVKAFYQKGNK--LVELMRIISRNGDT 117
Query: 119 EWFFNGKVVPKGEVLEITKRFNIQVNNLTQFLPQDRVCEFAKLSPVKLLEETEKAVGDPQ 178
+ +GK V + + NI + + Q V + A SPV+L E+ G Q
Sbjct: 118 SYKIDGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQ 177
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 939 HQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVR 988
+ SGGE++V+ + L ++ PF V+DE++ +D N +++ + R
Sbjct: 333 YLSGGEKTVAALALLFAINSYQPSPFFVLDEVDAALDITNVQRIAAYIRR 382
>pdb|3THO|A Chain A, Crystal Structure Of Mre11:rad50 In Its AtpADP BOUND STATE
Length = 382
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 47/172 (27%), Positives = 77/172 (44%), Gaps = 18/172 (10%)
Query: 12 SRGEDDYMPGNII--EIELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGG 69
S GE+ Y G++ + + NF+ ++ + S + +V GPNG+GKSSL AI+ AL G
Sbjct: 7 SSGENLYFQGHMRPERLTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFG 66
Query: 70 DTQLLGRATSIGAYVKRGEESGYIKISLRGDTKEEHLTIMRKIDTRNK------SEWFFN 123
+ R + YV R G ++ + + + I+R+I+ + SE N
Sbjct: 67 NGI---RYPNSYDYVNRNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILEN 123
Query: 124 GK-----VVPKGEVLEITKRFNIQVNNL--TQFLPQDRVCEFAKLSPVKLLE 168
GK P E+ K I+ T FLPQ + + P ++ E
Sbjct: 124 GKKAAIAAKPTSVKQEVEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITE 175
>pdb|3KTA|B Chain B, Structural Basis For Adenylate Kinase Activity In Abc
Atpases
pdb|3KTA|D Chain D, Structural Basis For Adenylate Kinase Activity In Abc
Atpases
Length = 173
Score = 43.1 bits (100), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 883 RNLVAQINETFSRNFQE----MAVAGEVSLDEHESDFDKFGILIKVKFRQSGQLEVLSAH 938
+N+ + E SRNF E ++ G L E+ D F ++++ + +G+ +V
Sbjct: 6 KNVFXRTFEAISRNFSEIFAKLSPGGSARLI-LENPEDPFSGGLEIEAKPAGK-DVKRIE 63
Query: 939 HQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAASQPNTPQC 998
SGGE++++ + ++ ++Q PF + DEI+ +D N +++ L++ +S+ + Q
Sbjct: 64 AXSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRV-ADLIKESSKES--QF 120
Query: 999 FLLTPKLLPDLEYSEACSILNI 1020
++T L D+ + A I+ +
Sbjct: 121 IVIT---LRDVXXANADKIIGV 139
>pdb|1XEW|Y Chain Y, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 883 RNLVAQINETFSRNFQE----MAVAGEVSLDEHESDFDKFGILIKVKFRQSGQLEVLSAH 938
+N+ + E SRNF E ++ G L E+ D F ++++ + +G+ +V
Sbjct: 5 KNVFMRTFEAISRNFSEIFAKLSPGGSARLI-LENPEDPFSGGLEIEAKPAGK-DVKRIE 62
Query: 939 HQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAASQPNTPQC 998
SGGE++++ + ++ ++Q PF + DEI+ +D N +++ L++ +S+ + Q
Sbjct: 63 AMSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRV-ADLIKESSKES--QF 119
Query: 999 FLLTPKLLPDLEYSEACSILNI 1020
++T L D+ + A I+ +
Sbjct: 120 IVIT---LRDVMMANADKIIGV 138
>pdb|1E69|A Chain A, Smc Head Domain From Thermotoga Maritima
pdb|1E69|B Chain B, Smc Head Domain From Thermotoga Maritima
pdb|1E69|C Chain C, Smc Head Domain From Thermotoga Maritima
pdb|1E69|D Chain D, Smc Head Domain From Thermotoga Maritima
pdb|1E69|E Chain E, Smc Head Domain From Thermotoga Maritima
pdb|1E69|F Chain F, Smc Head Domain From Thermotoga Maritima
Length = 322
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 61/114 (53%), Gaps = 10/114 (8%)
Query: 883 RNLVAQINETFSRNFQEMAVAGEVSLD---EHESDFDK-FGILIKVKFRQSGQLEVLSAH 938
R ++NE+F+R + GE L+ E +S D F I I+ R+ +L +LS
Sbjct: 164 RGSYQRVNESFNRFISLLFFGGEGRLNIVSEAKSILDAGFEISIRKPGRRDQKLSLLS-- 221
Query: 939 HQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAASQ 992
GGE+++ + L +L ++ PF V+DE++ +D N + F++L++ S+
Sbjct: 222 ---GGEKALVGLALLFALMEIKPSPFYVLDEVDSPLDDYNAER-FKRLLKENSK 271
Score = 38.5 bits (88), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 44 RLNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSIGAYVKRGEE----SGYIKISLRG 99
R+ ++GPNGSGKS+++ AI G ++ RA+ + G E +G + L
Sbjct: 25 RVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELRASEKFDMIFAGSENLPPAGSAYVELVF 84
Query: 100 DTKEEHLTIMRKIDTRNKSEWFFNGKVV 127
+ E +T+ R++ ++ ++ NG V
Sbjct: 85 EENGEEITVARELKRTGENTYYLNGSPV 112
>pdb|3QG5|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
pdb|3QG5|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
Length = 365
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 69/156 (44%), Gaps = 16/156 (10%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSIGAYVK 85
+ + NF+ ++ + S + +V GPNG+GKSSL AI+ AL G+ R + YV
Sbjct: 6 LTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGI---RYPNSYDYVN 62
Query: 86 RGEESGYIKISLRGDTKEEHLTIMRKIDTRNK------SEWFFNGK-----VVPKGEVLE 134
R G ++ + + + I+R+I+ + SE NGK P E
Sbjct: 63 RNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQE 122
Query: 135 ITKRFNIQVNNL--TQFLPQDRVCEFAKLSPVKLLE 168
+ K I+ T FLPQ + + P ++ E
Sbjct: 123 VEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITE 158
>pdb|3QF7|A Chain A, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
pdb|3QF7|B Chain B, The Mre11:rad50 Complex Forms An Atp Dependent Molecular
Clamp In Dna Double-Strand Break Repair
Length = 365
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 69/156 (44%), Gaps = 16/156 (10%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGGDTQLLGRATSIGAYVK 85
+ + NF+ ++ + S + +V GPNG+GKSSL AI+ AL G+ R + YV
Sbjct: 6 LTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGI---RYPNSYDYVN 62
Query: 86 RGEESGYIKISLRGDTKEEHLTIMRKIDTRNK------SEWFFNGK-----VVPKGEVLE 134
R G ++ + + + I+R+I+ + SE NGK P E
Sbjct: 63 RNAVDGTARLVFQFERGGKRYEIIREINALQRKHNAKLSEILENGKKAAIAAKPTSVKQE 122
Query: 135 ITKRFNIQVNNL--TQFLPQDRVCEFAKLSPVKLLE 168
+ K I+ T FLPQ + + P ++ E
Sbjct: 123 VEKILGIEHRTFIRTVFLPQGEIDKLLISPPSEITE 158
>pdb|1XEX|B Chain B, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 883 RNLVAQINETFSRNFQE----MAVAGEVSLDEHESDFDKFGILIKVKFRQSGQLEVLSAH 938
+N+ + E SRNF E ++ G L E+ D F ++++ + +G+ +V
Sbjct: 5 KNVFMRTFEAISRNFSEIFAKLSPGGSARLI-LENPEDPFSGGLEIEAKPAGK-DVKRIE 62
Query: 939 HQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAASQPNTPQC 998
SGGE++++ + ++ ++Q PF + D+I+ +D N +++ L++ +S+ + Q
Sbjct: 63 AMSGGEKALTALAFVFAIQKFKPAPFYLFDQIDAHLDDANVKRV-ADLIKESSKES--QF 119
Query: 999 FLLTPKLLPDLEYSEACSILNI 1020
++T L D+ + A I+ +
Sbjct: 120 IVIT---LRDVMMANADKIIGV 138
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|3ZGX|A Chain A, Crystal Structure Of The Kleisin-n Smc Interface In
Prokaryotic Condensin
pdb|3ZGX|B Chain B, Crystal Structure Of The Kleisin-n Smc Interface In
Prokaryotic Condensin
Length = 426
Score = 37.4 bits (85), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 73/161 (45%), Gaps = 10/161 (6%)
Query: 835 LNQNILQEYEHRQRQIEDLSTKQEADKKELKRFLAE-IDALKEKWLPTLRNLVAQINETF 893
+N + E+E + + LS ++E D E K L + I+ + E+ + QI F
Sbjct: 226 VNLGSIDEFERVNERYKFLSEQKE-DLTEAKNTLFQVIEEMDEEMTKRFNDTFVQIRSHF 284
Query: 894 SRNFQEMAVAGEVSL---DEHESDFDKFGILIKVKFRQSGQLEVLSAHHQSGGERSVSTI 950
+ F+ + G L D ++ I+ + ++ L +LS GGER+++ I
Sbjct: 285 DQVFRSLFGGGRAELRLTDPNDLLHSGVEIIAQPPGKKLQNLNLLS-----GGERALTAI 339
Query: 951 LYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLVRAAS 991
L S+ + PF V+DE+ +D N + Q L + +S
Sbjct: 340 ALLFSILKVRPVPFCVLDEVEAALDEANVFRFAQYLKKYSS 380
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 48 VIGPNGSGKSSLVCAIALALG 68
V+GPNGSGKS++ AI LG
Sbjct: 29 VVGPNGSGKSNITDAIRWVLG 49
>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 203
Score = 37.4 bits (85), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
Length = 359
Score = 37.0 bits (84), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
Length = 339
Score = 37.0 bits (84), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|1F2T|A Chain A, Crystal Structure Of Atp-free Rad50 Abc-atpase
pdb|1F2U|A Chain A, Crystal Structure Of Rad50 Abc-Atpase
pdb|1F2U|C Chain C, Crystal Structure Of Rad50 Abc-Atpase
Length = 149
Score = 36.2 bits (82), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|1US8|A Chain A, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 147
Score = 35.8 bits (81), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALAL 67
+ + NF + + + +NL+IG NGSGKSSL+ AI + L
Sbjct: 6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|1G9X|A Chain A, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
pdb|1G9X|B Chain B, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
pdb|1G9X|C Chain C, Characterization Of The Twinning Structure Of Mj1267, An
Atp-Binding Cassette Of An Abc Transporter
Length = 257
Score = 33.9 bits (76), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 38 ICKPGSRLNLVIGPNGSGKSSLVCAIALALGGD 70
+CK + L+IGPNGSGKS+L+ I L D
Sbjct: 30 VCK--GDVTLIIGPNGSGKSTLINVITGFLKAD 60
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 33.1 bits (74), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 23 IIEIELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGGD 70
+IE+ L N F + KP + L+ GP G+GK+ L A+A +G +
Sbjct: 196 VIELPLKNPEIFQRVGIKPPKGV-LLYGPPGTGKTLLAKAVAATIGAN 242
>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 = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 4/97 (4%)
Query: 378 ILELGVQANQKRLQKSEKEKILNQNKLTLRQCSDRLKD-MEDKNNKLLH-ALRNSGAENI 435
I ELG + + K + ++L +NK +DR+ D M K++ A R E +
Sbjct: 74 IKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQL 133
Query: 436 FEAYCWLQ--QHRHELNKEAYGPVLLEVNVSNRAHAN 470
F AYC ++ +H E + AY + + + N
Sbjct: 134 FTAYCNVEDAEHVKEAFRRAYNKITPSCRIDSSPAGN 170
>pdb|2O5V|A Chain A, Recombination Mediator Recf
Length = 359
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 25 EIELHNFMTFDHLICKPGSRLNL------VIGPNGSGKSSLVCAIALALGGDTQLLGRAT 78
++ L T ++ PG+ LN + G NG+GK++L+ A LAL G T A
Sbjct: 3 DVRLSALSTLNYRNLAPGT-LNFPEGVTGIYGENGAGKTNLLEAAYLALTGQTD----AP 57
Query: 79 SIGAYVKRGEESGYIKISL 97
I ++ GE Y++ L
Sbjct: 58 RIEQLIQAGETEAYVRADL 76
>pdb|1G6H|A Chain A, Crystal Structure Of The Adp Conformation Of Mj1267, An
Atp- Binding Cassette Of An Abc Transporter
Length = 257
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 45 LNLVIGPNGSGKSSLVCAIALALGGD 70
+ L+IGPNGSGKS+L+ I L D
Sbjct: 35 VTLIIGPNGSGKSTLINVITGFLKAD 60
>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 = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 378 ILELGVQANQKRLQKSEKEKILNQNKLTLRQCSDRLKD-MEDKNNKLLH-ALRNSGAENI 435
I ELG + + K + ++L +NK +DR+ D M K++ A R E +
Sbjct: 77 IKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQL 136
Query: 436 FEAYCWLQ--QHRHELNKEAYGPV 457
F AYC ++ +H E + AY +
Sbjct: 137 FTAYCNVEDAEHVKEAFRRAYNKI 160
>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 = 32.3 bits (72), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 378 ILELGVQANQKRLQKSEKEKILNQNKLTLRQCSDRLKD-MEDKNNKLLH-ALRNSGAENI 435
I ELG + + K + ++L +NK +DR+ D M K++ A R E +
Sbjct: 77 IKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQL 136
Query: 436 FEAYCWLQ--QHRHELNKEAYGPV 457
F AYC ++ +H E + AY +
Sbjct: 137 FTAYCNVEDAEHVKEAFRRAYNKI 160
>pdb|4AD8|A Chain A, Crystal Structure Of A Deletion Mutant Of Deinococcus
Radiodurans Recn
Length = 517
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGG 69
+E+ N T L + G G G+GKS +V A+ L LGG
Sbjct: 43 LEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGG 86
>pdb|2QEX|H Chain H, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 174
Score = 30.8 bits (68), Expect = 3.8, Method: Composition-based stats.
Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 4/97 (4%)
Query: 378 ILELGVQANQKRLQKSEKEKILNQNKLTLRQCSDRLKD-MEDKNNKLL-HALRNSGAENI 435
I ELG + + K + ++L +NK +DR+ D M K++ A R E +
Sbjct: 77 IKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQL 136
Query: 436 FEAYCWLQ--QHRHELNKEAYGPVLLEVNVSNRAHAN 470
F AYC ++ +H E + AY + + + N
Sbjct: 137 FTAYCNVEDAEHVKEAFRRAYNKITPSCRIDSSPAGN 173
>pdb|1GAJ|A Chain A, Crystal Structure Of A Nucleotide-Free Atp-Binding
Cassette From An Abc Transporter
Length = 257
Score = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 45 LNLVIGPNGSGKSSLVCAIALALGGD 70
+ L+IGPNGSGKS+L+ I L D
Sbjct: 35 VTLIIGPNGSGKSTLINVITGFLKAD 60
>pdb|4ABY|A Chain A, Crystal Structure Of Deinococcus Radiodurans Recn Head
Domain
pdb|4ABY|B Chain B, Crystal Structure Of Deinococcus Radiodurans Recn Head
Domain
pdb|4ABY|C Chain C, Crystal Structure Of Deinococcus Radiodurans Recn Head
Domain
pdb|4ABY|D Chain D, Crystal Structure Of Deinococcus Radiodurans Recn Head
Domain
Length = 415
Score = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 26 IELHNFMTFDHLICKPGSRLNLVIGPNGSGKSSLVCAIALALGG 69
+E+ N T L + G G G+GKS +V A+ L LGG
Sbjct: 43 LEIRNLATITQLELELGGGFCAFTGETGAGKSIIVDALGLLLGG 86
>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H
Length = 78
Score = 30.0 bits (66), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 126 VVPKGEVLEITKRFNIQVNNLTQFLPQDRVCE 157
+VPK EV EI KR+NI++ L + D V +
Sbjct: 14 IVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQ 45
>pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd
Length = 290
Score = 29.6 bits (65), Expect = 8.5, Method: Composition-based stats.
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 26/104 (25%)
Query: 928 QSGQLEVLSAHHQSGGERSVSTILYLVSLQDLTNCPFRVVDEINQGMDPINERKMFQQLV 987
QS L+ L A GG ++ S+ L ++ R++FQ L
Sbjct: 49 QSDDLQALLAERLEGGYKATSSARLLSAV-----------------------RRLFQYLY 85
Query: 988 RAASQPNTPQCFLLTPKLLPDL--EYSEACSILNIMNGPWIEQP 1029
R + + P L +PKL L + SEA + ++ P I+QP
Sbjct: 86 REKFREDDPSAHLASPKLPQRLPKDLSEA-QVERLLQAPLIDQP 128
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
0.316 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,007,381
Number of Sequences: 62578
Number of extensions: 1110179
Number of successful extensions: 3306
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 3240
Number of HSP's gapped (non-prelim): 76
length of query: 1051
length of database: 14,973,337
effective HSP length: 109
effective length of query: 942
effective length of database: 8,152,335
effective search space: 7679499570
effective search space used: 7679499570
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)