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= psy17514
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 91.7 bits (226), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 53/161 (32%), Positives = 90/161 (55%), Gaps = 8/161 (4%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVL-GIQVKQVRANT 60
YI+ + L GFKSYG + + F + F AI G NG+GKSNI D I FVL G+ K +RA+
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRASR 62
Query: 61 LQELIYKNG--QAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMING 118
+ +LI+ + A V + F+N D + PI +++ +VI R++ + Y +NG
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNED-RGFPI---DEDEVVIRRRVYPDGRSSYWLNG 118
Query: 119 SSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
+ D+ ++ ++ + + +++QG +TK + M P E
Sbjct: 119 RRATRSEILDILTAAMISPDG-YNIVLQGDITKFIKMSPLE 158
>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 = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 52/161 (32%), Positives = 88/161 (54%), Gaps = 8/161 (4%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVL-GIQVKQVRANT 60
YI+ + L GFKSYG + + F + F AI G NG+GKSNI D I FVL G+ K RA+
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASR 62
Query: 61 LQELIYKNG--QAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMING 118
+ +LI+ + A V + F+N D + PI +++ +VI R++ + Y +NG
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNED-RGFPI---DEDEVVIRRRVYPDGRSSYWLNG 118
Query: 119 SSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
+ D+ ++ ++ + + +++QG +TK + P E
Sbjct: 119 RRATRSEILDILTAAXISPDG-YNIVLQGDITKFIKXSPLE 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 = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 52/161 (32%), Positives = 88/161 (54%), Gaps = 8/161 (4%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVL-GIQVKQVRANT 60
YI+ + L GFKSYG + + F + F AI G NG+GKSNI D I FVL G+ K RA+
Sbjct: 3 YIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAXRASR 62
Query: 61 LQELIYKNG--QAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMING 118
+ +LI+ + A V + F+N D + PI +++ +VI R++ + Y +NG
Sbjct: 63 ISDLIFAGSKNEPPAKYAEVAIYFNNED-RGFPI---DEDEVVIRRRVYPDGRSSYWLNG 118
Query: 119 SSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
+ D+ ++ ++ + + +++QG +TK + P E
Sbjct: 119 RRATRSEILDILTAAXISPDG-YNIVLQGDITKFIKXSPLE 158
>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 = 79.0 bits (193), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 52/162 (32%), Positives = 82/162 (50%), Gaps = 16/162 (9%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQV-KQVRAN 59
M +K + L GFKS+G R + F AI G NG+GKSNI+D I +V G Q K++RA+
Sbjct: 1 MRLKKLYLKGFKSFG-RPSLIGFSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELRAS 59
Query: 60 TLQELIYKNGQ--AGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMIN 117
++I+ + A V L F+ EN I + R++ Y +N
Sbjct: 60 EKFDMIFAGSENLPPAGSAYVELVFE-----------ENGEEITVARELKRTGENTYYLN 108
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
GS V K + D F+ L V+ + ++ QG++ +++N P E
Sbjct: 109 GSPVRLKDIRDRFAGTGLGVDF-YSIVGQGQIDRIVNASPEE 149
>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 = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 50/162 (30%), Positives = 87/162 (53%), Gaps = 9/162 (5%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRAN 59
M++K + + GFKS+ R+ + DF + A+ G NG+GKSNI D I +VLG Q + +R
Sbjct: 1 MFLKRLDVIGFKSFAERISV-DFVKGVTAVVGPNGSGKSNITDAIRWVLGEQSARSLRGG 59
Query: 60 TLQELIY--KNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMIN 117
++++I+ + + + A VTLT DN D PI + + + + R++ + ++IN
Sbjct: 60 KMEDIIFAGSDSRKRLNLAEVTLTLDNDD-HFLPIDF---HEVSVTRRVYRSGESEFLIN 115
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
K + DLF L +I QG+V ++L+ K +
Sbjct: 116 NQPCRLKDIIDLFMDSGLG-KEAFSIISQGKVEEILSSKAED 156
>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 = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 52/162 (32%), Positives = 87/162 (53%), Gaps = 12/162 (7%)
Query: 6 MVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELI 65
+ L FKSY ++ + F +I G NG+GKSN++D I FVLG++ +R+N L++LI
Sbjct: 7 LELSNFKSYRGVTKVGFGESNFTSIIGPNGSGKSNMMDAISFVLGVRSNHLRSNILKDLI 66
Query: 66 YKNGQAGVTKASVTLTFDN-----SDKKNCPIG--YENDNTIV-ICRQISIPSNTRYMIN 117
Y+ GV + +DN S+ ++ + Y+ N +V + R IS +T Y I+
Sbjct: 67 YR----GVLNDENSDDYDNEGAASSNPQSAYVKAFYQKGNKLVELMRIISRNGDTSYKID 122
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
G +V+ K S + N+ + +FL+ QG V ++ P E
Sbjct: 123 GKTVSYKDYSIFLENENILIKAKNFLVFQGDVEQIAAQSPVE 164
>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 = 33.5 bits (75), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 71/166 (42%), Gaps = 28/166 (16%)
Query: 1 MYIKSMVLDGFKSY-GTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRAN 59
M +K + ++ FKS+ +R++ F++ AI G NG+GKS+I + + F L +N
Sbjct: 3 MILKEIRMNNFKSHVNSRIK---FEKGIVAIIGENGSGKSSIFEAVFFALF----GAGSN 55
Query: 60 TLQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGS 119
+ I G+ V V L F+ N N I R+ +
Sbjct: 56 FNYDTIITKGKKSVY---VELDFEV-----------NGNNYKIIREYDSGRGGAKLYKNG 101
Query: 120 SVNPKRVSDLFSSVN--LNVNNPHFL----IMQGRVTKVLNMKPHE 159
+S + +VN L V+ FL I QG + K L++KP E
Sbjct: 102 KPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSE 147
>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 = 29.6 bits (65), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>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 = 29.6 bits (65), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 29.6 bits (65), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>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 = 29.3 bits (64), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>pdb|1US8|A Chain A, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 147
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGIC 46
M ++ + + F+S+ V +F N I G NG+GKS++LD I
Sbjct: 1 MKLERVTVKNFRSHSDTV--VEFKEGINLIIGQNGSGKSSLLDAIL 44
>pdb|2O5V|A Chain A, Recombination Mediator Recf
Length = 359
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 23 FDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELIYKNGQAGVTKASV 78
F I G NG GK+N+L+ L Q A +++LI QAG T+A V
Sbjct: 24 FPEGVTGIYGENGAGKTNLLEAAYLAL---TGQTDAPRIEQLI----QAGETEAYV 72
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 0.136 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,539,170
Number of Sequences: 62578
Number of extensions: 174352
Number of successful extensions: 450
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 430
Number of HSP's gapped (non-prelim): 22
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
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: 47 (22.7 bits)