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= psy17517
(163 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 104 bits (259), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 49/79 (62%), Positives = 62/79 (78%)
Query: 85 AFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVL 144
A L E+ +EP+ G+ Y+ P KRF+ M LSGGEKTVAALALLFAI+SY P+PFFVL
Sbjct: 302 ASLTIEDEDEPFNAGIKYHATPPLKRFKDMEYLSGGEKTVAALALLFAINSYQPSPFFVL 361
Query: 145 DEIDAALDNTNIGKVASYI 163
DE+DAALD TN+ ++A+YI
Sbjct: 362 DEVDAALDITNVQRIAAYI 380
Score = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/50 (58%), Positives = 36/50 (72%)
Query: 10 AFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIH 59
A L E+ +EP+ G+ Y+ P KRF+ M LSGGEKTVAALALLFAI+
Sbjct: 302 ASLTIEDEDEPFNAGIKYHATPPLKRFKDMEYLSGGEKTVAALALLFAIN 351
>pdb|1XEW|Y Chain Y, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 48/74 (64%)
Query: 90 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDA 149
ENPE+P+ G+ GK + + +SGGEK + ALA +FAI + PAPF++ DEIDA
Sbjct: 37 ENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQKFKPAPFYLFDEIDA 96
Query: 150 ALDNTNIGKVASYI 163
LD+ N+ +VA I
Sbjct: 97 HLDDANVKRVADLI 110
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 15 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
ENPE+P+ G+ GK + + +SGGEK + ALA +FAI +
Sbjct: 37 ENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQK 82
>pdb|1XEX|B Chain B, Structural Biochemistry Of Atp-Driven Dimerization And Dna
Stimulated Activation Of Smc Atpases
Length = 172
Score = 76.6 bits (187), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 48/74 (64%)
Query: 90 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDA 149
ENPE+P+ G+ GK + + +SGGEK + ALA +FAI + PAPF++ D+IDA
Sbjct: 37 ENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQKFKPAPFYLFDQIDA 96
Query: 150 ALDNTNIGKVASYI 163
LD+ N+ +VA I
Sbjct: 97 HLDDANVKRVADLI 110
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 15 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
ENPE+P+ G+ GK + + +SGGEK + ALA +FAI +
Sbjct: 37 ENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQK 82
>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 = 76.3 bits (186), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 47/74 (63%)
Query: 90 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDA 149
ENPE+P+ G+ GK + + SGGEK + ALA +FAI + PAPF++ DEIDA
Sbjct: 38 ENPEDPFSGGLEIEAKPAGKDVKRIEAXSGGEKALTALAFVFAIQKFKPAPFYLFDEIDA 97
Query: 150 ALDNTNIGKVASYI 163
LD+ N+ +VA I
Sbjct: 98 HLDDANVKRVADLI 111
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 15 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
ENPE+P+ G+ GK + + SGGEK + ALA +FAI +
Sbjct: 38 ENPEDPFSGGLEIEAKPAGKDVKRIEAXSGGEKALTALAFVFAIQK 83
>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 = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 47/74 (63%)
Query: 90 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDA 149
ENPE+P+ G+ GK + + SGGEK + ALA +FAI + PAPF++ DEIDA
Sbjct: 219 ENPEDPFSGGLEIEAKPAGKDVKRIEAXSGGEKALTALAFVFAIQKFKPAPFYLFDEIDA 278
Query: 150 ALDNTNIGKVASYI 163
LD+ N+ +VA I
Sbjct: 279 HLDDANVKRVADLI 292
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 15 ENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
ENPE+P+ G+ GK + + SGGEK + ALA +FAI +
Sbjct: 219 ENPEDPFSGGLEIEAKPAGKDVKRIEAXSGGEKALTALAFVFAIQK 264
>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 = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 48/81 (59%)
Query: 83 AQAFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFF 142
+A L +P + GV PGK+ Q + LSGGE+ + A+ALLF+I P PF
Sbjct: 295 GRAELRLTDPNDLLHSGVEIIAQPPGKKLQNLNLLSGGERALTAIALLFSILKVRPVPFC 354
Query: 143 VLDEIDAALDNTNIGKVASYI 163
VLDE++AALD N+ + A Y+
Sbjct: 355 VLDEVEAALDEANVFRFAQYL 375
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 31/54 (57%)
Query: 8 AQAFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHRI 61
+A L +P + GV PGK+ Q + LSGGE+ + A+ALLF+I ++
Sbjct: 295 GRAELRLTDPNDLLHSGVEIIAQPPGKKLQNLNLLSGGERALTAIALLFSILKV 348
>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 = 63.9 bits (154), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 99 GVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
G + PG+R Q ++ LSGGEK + LALLFA+ P+PF+VLDE+D+ LD+ N
Sbjct: 202 GFEISIRKPGRRDQKLSLLSGGEKALVGLALLFALMEIKPSPFYVLDEVDSPLDDYN 258
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 24 GVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHRI 61
G + PG+R Q ++ LSGGEK + LALLFA+ I
Sbjct: 202 GFEISIRKPGRRDQKLSLLSGGEKALVGLALLFALMEI 239
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPF--FVLDEIDAALDNTNIGKVASYI 163
+P LSGGE+ + +++L ++ F +DE ++LD N K+AS +
Sbjct: 275 RPARGLSGGERALISISLAMSLAEVASGRLDAFFIDEGFSSLDTENKEKIASVL 328
>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 = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 112 QPMTNLSGGEKTVAALAL---LFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
+P LSGGE+ + +++L L + S FF+ DE ++LD N K+AS +
Sbjct: 275 RPARGLSGGERALISISLAXSLAEVASGRLDAFFI-DEGFSSLDTENKEKIASVL 328
>pdb|3B5X|A Chain A, Crystal Structure Of Msba From Vibrio Cholerae
pdb|3B5X|B Chain B, Crystal Structure Of Msba From Vibrio Cholerae
Length = 582
Score = 27.3 bits (59), Expect = 4.3, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 4/38 (10%)
Query: 115 TNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
T+LSGG++ A+A AP +LDE +ALD
Sbjct: 479 TSLSGGQRQRVAIARAL----LRDAPVLILDEATSALD 512
>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 = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSY---HPAPFFVLDEIDAALDNTNIGKVA 160
+ NLSGGE+ AL+L AI + + +LDE LD K+A
Sbjct: 277 TIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLA 327
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
0.317 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,636,808
Number of Sequences: 62578
Number of extensions: 164288
Number of successful extensions: 603
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 586
Number of HSP's gapped (non-prelim): 25
length of query: 163
length of database: 14,973,337
effective HSP length: 91
effective length of query: 72
effective length of database: 9,278,739
effective search space: 668069208
effective search space used: 668069208
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)