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= 001328
(1099 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WD5|B Chain B, Smc Hinge Heterodimer (Mouse)
Length = 213
Score = 172 bits (436), Expect = 9e-43, Method: Compositional matrix adjust.
Identities = 79/188 (42%), Positives = 124/188 (65%), Gaps = 9/188 (4%)
Query: 489 EVEKAEKSLDHATPGDVRRGLNSIRRICREYKIDGV--------YGPIIELLDCDEKFFT 540
++EK ++ L AT + G++SI ++ ++ G+ +G ++ +C+ F+T
Sbjct: 6 DLEKKQQLLRAATGKAILNGIDSINKVLEHFRRKGINQHVQNGYHGIVMNNFECEPAFYT 65
Query: 541 AVEVTAGNSLFHVVVDNDETSTKIIRHLNSLK-GGRVTFIPLNRVKAPRVTYPKSNDVIP 599
VEVTAGN LF+ +VD+DE STKI+ N + G VTF+PLN++ YP++ND IP
Sbjct: 66 CVEVTAGNRLFYHIVDSDEVSTKILMEFNKMNLPGEVTFLPLNKLDVRDTAYPETNDAIP 125
Query: 600 LLDRLEFSPNFKPAFAQVFARTVICRDLDVCTRVARTDGLDCITLEGDQVSKKGGMTGGF 659
++ +L ++P F AF VF +T+ICR ++V T++AR +DCITLEGDQVS +G +TGG+
Sbjct: 126 MISKLRYNPRFDKAFKHVFGKTLICRSMEVSTQLARAFTMDCITLEGDQVSHRGALTGGY 185
Query: 660 YDYRRSKL 667
YD R+S+L
Sbjct: 186 YDTRKSRL 193
>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 = 93.6 bits (231), Expect = 5e-19, Method: Composition-based stats.
Identities = 58/180 (32%), Positives = 104/180 (57%), Gaps = 5/180 (2%)
Query: 2 HIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDI-FQNLRSED 60
+I+++ ++GFKSY + PFS +VGANGSGK+N AI FVL + + +R+
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRASR 62
Query: 61 RHALLHEGAGHQVLSAFVE--IVFDNSDNRIPVDKEEVRLRRTIGLK-KDEYFLDGKHIT 117
L+ G+ ++ + + E I F+N D P+D++EV +RR + + Y+L+G+ T
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRAT 122
Query: 118 KTEVMNLLESAGFSRSNPYYVVQQGKIASLTLMKDSERLDLLKEIGGTRVYEERRRESLK 177
++E++++L +A S + Y +V QG I M ER L+ +I G Y+ ++ ++L+
Sbjct: 123 RSEILDILTAAMIS-PDGYNIVLQGDITKFIKMSPLERRLLIDDISGIAEYDSKKEKALE 181
>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 = 90.1 bits (222), Expect = 6e-18, Method: Composition-based stats.
Identities = 57/180 (31%), Positives = 101/180 (56%), Gaps = 5/180 (2%)
Query: 2 HIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSEDR 61
+I+++ ++GFKSY + PFS +VGANGSGK+N AI FVL + R
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASR 62
Query: 62 HA-LLHEGAGHQVLSAFVE--IVFDNSDNRIPVDKEEVRLRRTIGLK-KDEYFLDGKHIT 117
+ L+ G+ ++ + + E I F+N D P+D++EV +RR + + Y+L+G+ T
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRAT 122
Query: 118 KTEVMNLLESAGFSRSNPYYVVQQGKIASLTLMKDSERLDLLKEIGGTRVYEERRRESLK 177
++E++++L +A S + Y +V QG I ER L+ +I G Y+ ++ ++L+
Sbjct: 123 RSEILDILTAAXIS-PDGYNIVLQGDITKFIKXSPLERRLLIDDISGIAEYDSKKEKALE 181
>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 = 85.1 bits (209), Expect = 2e-16, Method: Composition-based stats.
Identities = 56/172 (32%), Positives = 95/172 (55%), Gaps = 5/172 (2%)
Query: 2 HIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSEDR 61
+I+++ ++GFKSY + PFS +VGANGSGK+N AI FVL + R
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASR 62
Query: 62 HA-LLHEGAGHQVLSAFVE--IVFDNSDNRIPVDKEEVRLRRTIGLK-KDEYFLDGKHIT 117
+ L+ G+ ++ + + E I F+N D P+D++EV +RR + + Y+L+G+ T
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRAT 122
Query: 118 KTEVMNLLESAGFSRSNPYYVVQQGKIASLTLMKDSERLDLLKEIGGTRVYE 169
++E++++L +A S + Y +V QG I ER L+ +I G Y+
Sbjct: 123 RSEILDILTAAXIS-PDGYNIVLQGDITKFIKXSPLERRLLIDDISGIAEYD 173
Score = 31.2 bits (69), Expect = 3.2, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 1018 RTFKGVARHFREVFSELVQGGHGHLVM 1044
RTF+ ++R+F E+F++L GG L++
Sbjct: 192 RTFEAISRNFSEIFAKLSPGGSARLIL 218
>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 = 74.7 bits (182), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 55/198 (27%), Positives = 105/198 (53%), Gaps = 9/198 (4%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSD-IFQNLRSE 59
M +K++ + GFKS+ E+I+ + F V VVG NGSGK+N AIR+VL + ++LR
Sbjct: 1 MFLKRLDVIGFKSFAERISVD-FVKGVTAVVGPNGSGKSNITDAIRWVLGEQSARSLRGG 59
Query: 60 DRHALLHEGAGH--QVLSAFVEIVFDNSDNRIPVDKEEVRL-RRTIGLKKDEYFLDGKHI 116
++ G+ ++ A V + DN D+ +P+D EV + RR + E+ ++ +
Sbjct: 60 KMEDIIFAGSDSRKRLNLAEVTLTLDNDDHFLPIDFHEVSVTRRVYRSGESEFLINNQPC 119
Query: 117 TKTEVMNLLESAGFSRSNPYYVVQQGKIASLTLMKDSERLDLLKEIGGTRVYEERRRES- 175
++++L +G + + ++ QGK+ + K +R + +E G Y+ R++++
Sbjct: 120 RLKDIIDLFMDSGLGK-EAFSIISQGKVEEILSSKAEDRRSIFEEAAGVLKYKTRKKKAE 178
Query: 176 --LKIMQDTGNKRQQIIQ 191
L QD N+ + I+
Sbjct: 179 NKLFETQDNLNRVEDILH 196
>pdb|3NWC|A Chain A, Crystal Structure Of The Pyrococcus Furiosus Smc Protein
Hinge Domain
pdb|3NWC|B Chain B, Crystal Structure Of The Pyrococcus Furiosus Smc Protein
Hinge Domain
Length = 189
Score = 72.8 bits (177), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 45/144 (31%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 521 IDGVYGPIIELLDC-DEKFFTAVEVTAGNSLFHVVVDNDETSTKIIRHLNSLKGGRVTFI 579
I G+YG + EL+ DE + A+EV GN +VVV+++ + K I++L K GR+TF+
Sbjct: 33 IGGIYGTLAELIKVKDEAYALAIEVALGNRADNVVVEDELVAEKAIKYLKEHKLGRLTFL 92
Query: 580 PLNRVKAPRVTYPKSNDVIPLLDRLEFSPNFKPAFAQVFARTVICRDLDVCTRVARTDGL 639
PLN++K V S+ +P +D +E+ + A TVI + +
Sbjct: 93 PLNKIKPKHV---DSSVGLPAVDVIEYDQKIENAVKFALGDTVIVNSXEEAR--PHIGKV 147
Query: 640 DCITLEGDQVSKKGGMTGGFYDYR 663
+T+EG+ + G +TGG + R
Sbjct: 148 RXVTIEGELYERSGAITGGHFRAR 171
>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 = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 45/148 (30%), Positives = 83/148 (56%), Gaps = 13/148 (8%)
Query: 1 MHIKQVIIEGFKSY-REQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQN-LRS 58
M +K++ ++GFKS+ R + FS +V +VG NGSGK+N AI++V + + LR+
Sbjct: 1 MRLKKLYLKGFKSFGRPSLIG--FSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELRA 58
Query: 59 EDRHALLHEGAGH--QVLSAFVEIVFDNSDNRIPVDKEEVRLRRTIGLKKDEYFLDGKHI 116
++ ++ G+ + SA+VE+VF+ + I V +E L+RT ++ Y+L+G +
Sbjct: 59 SEKFDMIFAGSENLPPAGSAYVELVFEENGEEITVARE---LKRT---GENTYYLNGSPV 112
Query: 117 TKTEVMNLLESAGFSRSNPYYVVQQGKI 144
++ + G + Y +V QG+I
Sbjct: 113 RLKDIRDRFAGTGLG-VDFYSIVGQGQI 139
>pdb|1GXL|A Chain A, Smc Hinge Domain From T. Maritima With Coiled Coil
pdb|1GXL|B Chain B, Smc Hinge Domain From T. Maritima With Coiled Coil
pdb|1GXL|C Chain C, Smc Hinge Domain From T. Maritima With Coiled Coil
pdb|1GXL|D Chain D, Smc Hinge Domain From T. Maritima With Coiled Coil
Length = 213
Score = 57.8 bits (138), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 44/160 (27%), Positives = 80/160 (50%), Gaps = 8/160 (5%)
Query: 507 RGLNSIRRICREYK--IDGVYGPIIELLDCDEKFFTAVEVTAGNSLFHVVVDNDETSTKI 564
RG + R E K G+ + L++ DEK+ AV V G + ++VV N +T+ I
Sbjct: 25 RGFSRAVRAVFEEKERFPGLVDVVSNLIEVDEKYSLAVSVLLGGTAQNIVVRNVDTAKAI 84
Query: 565 IRHLNSLKGGRVTFIPLNRVKAP--RVTYPKS--NDVIPLLDRLEFSPNFKPAFAQVFAR 620
+ L + GRVT +PL+ + R++ ++ V +D ++F + + +F
Sbjct: 85 VEFLKQNEAGRVTILPLDLIDGSFNRISGLENERGFVGYAVDLVKFPSDLEVLGGFLFGN 144
Query: 621 TVICRDLDVCTRVARTDGLD--CITLEGDQVSKKGGMTGG 658
+V+ LD R+ + L+ TL+G+ +S +G +TGG
Sbjct: 145 SVVVETLDDAIRMKKKYRLNTRIATLDGELISGRGAITGG 184
>pdb|1GXJ|A Chain A, Smc Hinge Domain From T. Maritima WO COILED COIL
pdb|1GXJ|B Chain B, Smc Hinge Domain From T. Maritima WO COILED COIL
pdb|1GXK|A Chain A, Smc Hinge Domain From T. Maritima WO COILED COIL, P212121
Crystal Form
pdb|1GXK|B Chain B, Smc Hinge Domain From T. Maritima WO COILED COIL, P212121
Crystal Form
pdb|1GXK|C Chain C, Smc Hinge Domain From T. Maritima WO COILED COIL, P212121
Crystal Form
pdb|1GXK|D Chain D, Smc Hinge Domain From T. Maritima WO COILED COIL, P212121
Crystal Form
Length = 186
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 75/145 (51%), Gaps = 6/145 (4%)
Query: 520 KIDGVYGPIIELLDCDEKFFTAVEVTAGNSLFHVVVDNDETSTKIIRHLNSLKGGRVTFI 579
+ G+ + L++ DEK+ AV V G + ++VV N +T+ I+ L + GRVT +
Sbjct: 28 RFPGLVDVVSNLIEVDEKYSLAVSVLLGGTAQNIVVRNVDTAKAIVEFLKQNEAGRVTIL 87
Query: 580 PLNRVKAP--RVTYPKS--NDVIPLLDRLEFSPNFKPAFAQVFARTVICRDLDVCTRVAR 635
PL+ + R++ ++ V +D ++F + + +F +V+ LD R+ +
Sbjct: 88 PLDLIDGSFNRISGLENERGFVGYAVDLVKFPSDLEVLGGFLFGNSVVVETLDDAIRMKK 147
Query: 636 TDGLD--CITLEGDQVSKKGGMTGG 658
L+ TL+G+ +S +G +TGG
Sbjct: 148 KYRLNTRIATLDGELISGRGAITGG 172
>pdb|3L51|B Chain B, Crystal Structure Of The Mouse Condensin Hinge Domain
Length = 166
Score = 47.4 bits (111), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 42/146 (28%), Positives = 74/146 (50%), Gaps = 7/146 (4%)
Query: 520 KIDGVYGPIIELLDCDEKFFTAVEVTAGNSLFHVVVDNDETSTKIIRHLNSLKGGRVTFI 579
+I G+YG + +L DEK+ A+ + ++L ++VVD+ +T+ + + L G TFI
Sbjct: 15 RIPGIYGRLGDLGAIDEKYDIAIS-SCCHALDYIVVDSIDTAQECVNFLKKHNIGIATFI 73
Query: 580 PLNR--VKAPRVTYPKSNDVIPLLDRLEFSPN--FKPAFAQVFARTVICRDLDVCTRVA- 634
L++ V A + + ++ + P L L N + AF T++ +LD TRVA
Sbjct: 74 GLDKXTVWAKKXSKIQTPENTPRLFDLVKVKNEEIRQAFYFALRDTLVANNLDQATRVAY 133
Query: 635 -RTDGLDCITLEGDQVSKKGGMTGGF 659
R +TL+G + + G +GG
Sbjct: 134 QRDRRWRVVTLQGQIIEQSGTXSGGL 159
>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 = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 45/174 (25%), Positives = 69/174 (39%), Gaps = 23/174 (13%)
Query: 8 IEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSEDRHALLHE 67
+ FKSYR ++G NGSGK+N AI FVL +LRS L++
Sbjct: 9 LSNFKSYRGVTKVGFGESNFTSIIGPNGSGKSNMMDAISFVLGVRSNHLRSNILKDLIYR 68
Query: 68 G---------------AGHQVLSAFVEIVFDNSDNRIPVDKEEVRLRRTIGLKKD-EYFL 111
G A SA+V+ F N++ V L R I D Y +
Sbjct: 69 GVLNDENSDDYDNEGAASSNPQSAYVK-AFYQKGNKL------VELMRIISRNGDTSYKI 121
Query: 112 DGKHITKTEVMNLLESAGFSRSNPYYVVQQGKIASLTLMKDSERLDLLKEIGGT 165
DGK ++ + LE+ ++V QG + + E + +E+ G+
Sbjct: 122 DGKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGS 175
>pdb|2WD5|A Chain A, Smc Hinge Heterodimer (Mouse)
Length = 233
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/146 (23%), Positives = 68/146 (46%), Gaps = 6/146 (4%)
Query: 524 VYGPIIELL-DCDEKFFTAVEVTAGNSLFHVVVDNDETSTKIIRHLNSLKGGRVTFIPLN 582
VYG +I+L +K+ AV G ++ ++VD+++T I+++ +G TF+PL+
Sbjct: 55 VYGRLIDLCQPTQKKYQIAVTKVLGKNMDAIIVDSEKTGRDCIQYIKEQRGEPETFLPLD 114
Query: 583 --RVKAPRVTYPKSNDVIPLLDRLEF-SPNFKPAFAQVFARTVICRDLDVCTRVARTDGL 639
VK + ++D + + P+ K A ++C +++ R+A
Sbjct: 115 YLEVKPTDEKLRELKGAKLVIDVIRYEPPHIKKALQYACGNALVCDNVEDARRIAFGGHQ 174
Query: 640 --DCITLEGDQVSKKGGMTGGFYDYR 663
+ L+G K G ++GG D +
Sbjct: 175 RHKTVALDGTLFQKSGVISGGASDLK 200
>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 = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 21/175 (12%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +K++ + FKS+ + F + ++G NGSGK++ F A+ F L N +
Sbjct: 3 MILKEIRMNNFKSHVN--SRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYD- 59
Query: 61 RHALLHEGAGHQVLSAFVEIVFDNSDNRIPVDKEEVRLRRTIGLKKDEYFLDGK-HITKT 119
++ +G S +VE+ F+ + N + +E R L K +GK + T
Sbjct: 60 --TIITKGKK----SVYVELDFEVNGNNYKIIREYDSGRGGAKLYK-----NGKPYATTI 108
Query: 120 EVMN--LLESAGFSRS---NPYYVVQQGKIASLTLMKDSERLDLLKEIGGTRVYE 169
+N + E G R+ N Y ++QG+IA +K SE+L+ + ++ G +E
Sbjct: 109 SAVNKAVNEILGVDRNMFLNSIY-IKQGEIAKFLSLKPSEKLETVAKLLGIDEFE 162
Score = 29.6 bits (65), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 366 MEREKQLSILYQKQGRATQFSSKDARDKW--LQK--EIDDLERVHSSNLKQDQKLQEEIQ 421
++R L+ +Y KQG +F S +K + K ID+ E+ + + ++ ++ ++
Sbjct: 121 VDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLE 180
Query: 422 RLKGDLKERDEYIESRKREIAYLE 445
R++G+L ++E +++R +E++ LE
Sbjct: 181 RIEGELNYKEESLKARLKEMSNLE 204
>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 = 0.062, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVVE--FKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>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 = 0.063, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVVE--FKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 37.0 bits (84), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>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 = 36.6 bits (83), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>pdb|3QE6|A Chain A, Mouse Pacsin 3 F-Bar Domain Structure
pdb|3QE6|B Chain B, Mouse Pacsin 3 F-Bar Domain Structure
Length = 304
Score = 35.8 bits (81), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 58/138 (42%), Gaps = 9/138 (6%)
Query: 231 ELH-DARQKLLEVDDTRTRFSDESAKMYNSLLDAQEKSKDSDKRFKDLMKEVQTLNKEKE 289
ELH + R+KL D R R A + +L +S+ ++ F+ K KE E
Sbjct: 93 ELHLEVREKLHGPDSERVRTWQRGA-FHRPVLGGFRESRAAEDGFRKAQKPWLKRLKEVE 151
Query: 290 AIEKRLTEAIKNQTAFELDVKDIQERISGNSQARDDAKKQLRSLLEEIDDSSKELDKANT 349
A +K A K D K Q R S +++QLR L E + +KE +K T
Sbjct: 152 ASKKSYHTARK-------DEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKT 204
Query: 350 LYENKCIEEKKITKDIME 367
YE E + T ME
Sbjct: 205 QYEQTLAELNRYTPRYME 222
>pdb|3SYV|A Chain A, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|B Chain B, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|C Chain C, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|D Chain D, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|E Chain E, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|F Chain F, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|G Chain G, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
pdb|3SYV|H Chain H, Crystal Structure Of Mpacsin 3 F-Bar Domain Mutant
Length = 347
Score = 35.4 bits (80), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 58/138 (42%), Gaps = 9/138 (6%)
Query: 231 ELH-DARQKLLEVDDTRTRFSDESAKMYNSLLDAQEKSKDSDKRFKDLMKEVQTLNKEKE 289
ELH + R+KL D R R A + +L +S+ ++ F+ K KE E
Sbjct: 99 ELHLEVREKLHGPDSERVRTWQRGA-FHRQVLGGFRESRAAEDGFRKAQKPWLKRLKEVE 157
Query: 290 AIEKRLTEAIKNQTAFELDVKDIQERISGNSQARDDAKKQLRSLLEEIDDSSKELDKANT 349
A +K A K D K Q R S +++QLR L E + +KE +K T
Sbjct: 158 ASKKSYHTARK-------DEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKT 210
Query: 350 LYENKCIEEKKITKDIME 367
YE E + T ME
Sbjct: 211 QYEQTLAELNRYTPRYME 228
>pdb|3M3W|A Chain A, Crystal Strcuture Of Mouse Pacsin3 Bar Domain Mutant
pdb|3M3W|B Chain B, Crystal Strcuture Of Mouse Pacsin3 Bar Domain Mutant
Length = 320
Score = 35.4 bits (80), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 57/138 (41%), Gaps = 9/138 (6%)
Query: 231 ELH-DARQKLLEVDDTRTRFSDESAKMYNSLLDAQEKSKDSDKRFKDLMKEVQTLNKEKE 289
ELH + R+KL D R R A + +L S+ ++ F+ K KE E
Sbjct: 93 ELHLEVREKLHGPDSERVRTWQRGA-FHRPVLGGFRASRAAEDGFRKAQKPWLKRLKEVE 151
Query: 290 AIEKRLTEAIKNQTAFELDVKDIQERISGNSQARDDAKKQLRSLLEEIDDSSKELDKANT 349
A +K A K D K Q R S +++QLR L E + +KE +K T
Sbjct: 152 ASKKSYHTARK-------DEKTAQTRESHAKADSSMSQEQLRKLQERVGRCTKEAEKMKT 204
Query: 350 LYENKCIEEKKITKDIME 367
YE E + T ME
Sbjct: 205 QYEQTLAELNRYTPRYME 222
>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 = 35.0 bits (79), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>pdb|1US8|A Chain A, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 147
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 MHIKQVIIEGFKSYREQIATEPFSPQVNCVVGANGSGKTNFFHAIRFVLSDIFQNLRSED 60
M +++V ++ F+S+ + + F +N ++G NGSGK++ AI L ++ LR +D
Sbjct: 1 MKLERVTVKNFRSHSDTVVE--FKEGINLIIGQNGSGKSSLLDAI---LVGLYWPLRIKD 55
>pdb|1XEX|B Chain B, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 33.9 bits (76), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 1018 RTFKGVARHFREVFSELVQGGHGHLVMMXXXXXXXXXXXXXXXPRESDVEGRVEKYIGVK 1077
RTF+ ++R+F E+F++L GG L++ P DV+ R+E G +
Sbjct: 10 RTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVK-RIEAMSGGE 68
Query: 1078 VKACTSVKMNSFAF 1091
KA T++ +F F
Sbjct: 69 -KALTAL---AFVF 78
>pdb|1XEW|Y Chain Y, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 33.5 bits (75), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 1018 RTFKGVARHFREVFSELVQGGHGHLVMMXXXXXXXXXXXXXXXPRESDVEGRVEKYIGVK 1077
RTF+ ++R+F E+F++L GG L++ P DV+ R+E G +
Sbjct: 10 RTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVK-RIEAMSGGE 68
Query: 1078 VKACTSVKMNSFAF 1091
KA T++ +F F
Sbjct: 69 -KALTAL---AFVF 78
>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 = 33.5 bits (75), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 1018 RTFKGVARHFREVFSELVQGGHGHLVMMXXXXXXXXXXXXXXXPRESDVEGRVEKYIGVK 1077
RTF+ ++R+F E+F++L GG L++ P DV+ R+E G +
Sbjct: 11 RTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVK-RIEAXSGGE 69
Query: 1078 VKACTSVKMNSFAF 1091
KA T++ +F F
Sbjct: 70 -KALTAL---AFVF 79
>pdb|3ZIL|B Chain B, Structure Of The Wpl1 Protein
Length = 28
Score = 32.7 bits (73), Expect = 1.1, Method: Composition-based stats.
Identities = 16/28 (57%), Positives = 21/28 (75%)
Query: 134 NPYYVVQQGKIASLTLMKDSERLDLLKE 161
NPY +V QG+I SLT ++ ERL LL+E
Sbjct: 1 NPYNIVPQGRIVSLTNAQNRERLQLLEE 28
>pdb|1XSZ|A Chain A, The Structure Of Ralf
pdb|1XSZ|B Chain B, The Structure Of Ralf
Length = 356
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 488 AEVEKAEKSLDHATPGDVRRGLNSIRRICREYKI 521
E+EKA++ + A + G+N I+ IC +YKI
Sbjct: 5 PEIEKAQREIIEAFNAKPKNGINKIKEICEQYKI 38
>pdb|1XT0|B Chain B, The Structure Of N-Terminal Sec7 Domain Of Ralf
Length = 203
Score = 32.7 bits (73), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 488 AEVEKAEKSLDHATPGDVRRGLNSIRRICREYKI 521
E+EKA++ + A + G+N I+ IC +YKI
Sbjct: 5 PEIEKAQREIIEAFNAKPKNGINKIKEICEQYKI 38
>pdb|1REQ|B Chain B, Methylmalonyl-Coa Mutase
pdb|1REQ|D Chain D, Methylmalonyl-Coa Mutase
pdb|2REQ|B Chain B, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|D Chain D, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|B Chain B, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|B Chain B, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|D Chain D, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|B Chain B, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|D Chain D, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|B Chain B, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|D Chain D, Methylmalonyl-Coa Mutase Substrate Complex
pdb|5REQ|B Chain B, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|D Chain D, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|1E1C|B Chain B, Methylmalonyl-Coa Mutase H244a Mutant
pdb|1E1C|D Chain D, Methylmalonyl-Coa Mutase H244a Mutant
Length = 637
Score = 31.2 bits (69), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 13/128 (10%)
Query: 628 DVCTRVARTDGLDCITLEGDQVSKKGGMTGGFYDYRRSKLKFMNIIMRNTKTINARE-EE 686
D R+AR G+ + E + + GG Y ++ + R+ +E +E
Sbjct: 372 DFPLRIARNTGI--VLAEEVNIGRVNDPAGGSY--------YVESLTRSLADAAWKEFQE 421
Query: 687 VEKLISQLDQKITEHVTEQQKTDAKRAHDKSELEQLKQDIANANKQKQIISKALENKEKS 746
VEKL +TEHVT + DA A L KQ I ++ I ++++E K
Sbjct: 422 VEKLGGMSKAVMTEHVT--KVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFP 479
Query: 747 LADVRTQL 754
A R L
Sbjct: 480 AAPARKGL 487
>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 = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 23 FSPQVNCVVGANGSGKTNFFHAIRFVL 49
F + V G NG+GK++ F AI F L
Sbjct: 21 FQSGITVVEGPNGAGKSSLFEAISFAL 47
>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 = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 23 FSPQVNCVVGANGSGKTNFFHAIRFVL 49
F + V G NG+GK++ F AI F L
Sbjct: 21 FQSGITVVEGPNGAGKSSLFEAISFAL 47
>pdb|3THO|A Chain A, Crystal Structure Of Mre11:rad50 In Its AtpADP BOUND
STATE
Length = 382
Score = 30.4 bits (67), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 23 FSPQVNCVVGANGSGKTNFFHAIRFVL 49
F + V G NG+GK++ F AI F L
Sbjct: 38 FQSGITVVEGPNGAGKSSLFEAISFAL 64
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
0.314 0.131 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,089,156
Number of Sequences: 62578
Number of extensions: 1113600
Number of successful extensions: 3854
Number of sequences better than 100.0: 181
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 132
Number of HSP's that attempted gapping in prelim test: 3479
Number of HSP's gapped (non-prelim): 462
length of query: 1099
length of database: 14,973,337
effective HSP length: 109
effective length of query: 990
effective length of database: 8,152,335
effective search space: 8070811650
effective search space used: 8070811650
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 57 (26.6 bits)