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= psy9513
(1491 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.8 bits (107), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 9/63 (14%)
Query: 14 NFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFALTNEYPQGASSGKNFVHDPRI-- 71
NF + N ++F++ + I+GENG GK++I E + FAL +G NF +D I
Sbjct: 12 NFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALF-------GAGSNFNYDTIITK 64
Query: 72 GKK 74
GKK
Sbjct: 65 GKK 67
>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 = 43.5 bits (101), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFALTN---EYP 56
+RNF KN + FQ +T++ G NG GK+++ E I FAL YP
Sbjct: 8 VRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYP 55
>pdb|3THO|A Chain A, Crystal Structure Of Mre11:rad50 In Its AtpADP BOUND
STATE
Length = 382
Score = 43.1 bits (100), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFALTN---EYP 56
+RNF KN + FQ +T++ G NG GK+++ E I FAL YP
Sbjct: 25 VRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFALFGNGIRYP 72
>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 = 39.3 bits (90), Expect = 0.016, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 27/42 (64%)
Query: 10 MGIRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
+ +RNF KN + FQ +T++ G NG GK+++ E I FAL
Sbjct: 6 LTVRNFLGLKNVDIEFQSGITVVEGPNGAGKSSLFEAISFAL 47
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 38.5 bits (88), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 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 = 38.5 bits (88), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 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 = 38.5 bits (88), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>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 = 38.5 bits (88), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 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 = 38.1 bits (87), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|1US8|A Chain A, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 147
Score = 37.7 bits (86), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 27/40 (67%)
Query: 12 IRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
++NF + + VV F+ + LI+G+NG GK+++++ I L
Sbjct: 8 VKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
>pdb|2IWH|A Chain A, Structure Of Yeast Elongation Factor 3 In Complex With Adpnp
pdb|2IWH|B Chain B, Structure Of Yeast Elongation Factor 3 In Complex With Adpnp
pdb|2IX3|A Chain A, Structure Of Yeast Elongation Factor 3
pdb|2IX3|B Chain B, Structure Of Yeast Elongation Factor 3
Length = 986
Score = 37.7 bits (86), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 44/95 (46%), Gaps = 11/95 (11%)
Query: 1225 DEEFIENLTAIDRAYVVRIVRDHKALAETFSRNCGIFALDEPTTNLDIKNASDQKNF--- 1281
DE ++A+ + +++ ALA RN I LDEPT +LD N + N+
Sbjct: 539 DEMIAMPISALSGGWKMKL-----ALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNT 593
Query: 1282 ---QLIVITHDEEFIENLTAIDRAYVVRIVRDHKG 1313
I I+HD F++N+ Y +R +KG
Sbjct: 594 CGITSITISHDSVFLDNVCEYIINYEGLKLRKYKG 628
Score = 30.0 bits (66), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 1260 IFALDEPTTNLD------IKNASDQKNFQLIVITHDEEFIENLT 1297
+ LDEPT LD + A + +I+ITH EF +NLT
Sbjct: 922 LIVLDEPTNYLDRDSLGALSKALKEFEGGVIIITHSAEFTKNLT 965
>pdb|2IW3|A Chain A, Elongation Factor 3 In Complex With Adp
pdb|2IW3|B Chain B, Elongation Factor 3 In Complex With Adp
Length = 986
Score = 37.7 bits (86), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 11/95 (11%)
Query: 1225 DEEFIENLTAIDRAYVVRIVRDHKALAETFSRNCGIFALDEPTTNLDIKNASDQKNF--- 1281
DE ++A+ + ++ ALA RN I LDEPT +LD N + N+
Sbjct: 539 DEXIAXPISALSGGWKXKL-----ALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNT 593
Query: 1282 ---QLIVITHDEEFIENLTAIDRAYVVRIVRDHKG 1313
I I+HD F++N+ Y +R +KG
Sbjct: 594 CGITSITISHDSVFLDNVCEYIINYEGLKLRKYKG 628
>pdb|2IX8|A Chain A, Model For Eef3 Bound To An 80s Ribosome
Length = 976
Score = 37.4 bits (85), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 11/95 (11%)
Query: 1225 DEEFIENLTAIDRAYVVRIVRDHKALAETFSRNCGIFALDEPTTNLDIKNASDQKNF--- 1281
DE ++A+ + ++ ALA RN I LDEPT +LD N + N+
Sbjct: 533 DEXIAXPISALSGGWKXKL-----ALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNT 587
Query: 1282 ---QLIVITHDEEFIENLTAIDRAYVVRIVRDHKG 1313
I I+HD F++N+ Y +R +KG
Sbjct: 588 CGITSITISHDSVFLDNVCEYIINYEGLKLRKYKG 622
>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 = 37.0 bits (84), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 3 LLDQLHIMGIRNFPADKNRV-VRFQRPLTLIVGENGCGKTTIIECIKFALTNEYPQGASS 61
L +L ++G ++F R+ V F + +T +VG NG GK+ I + I++ L + +
Sbjct: 2 FLKRLDVIGFKSFA---ERISVDFVKGVTAVVGPNGSGKSNITDAIRWVLGEQSARSLRG 58
Query: 62 GK 63
GK
Sbjct: 59 GK 60
>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 = 35.8 bits (81), Expect = 0.17, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 1 MALLDQLHIMGIRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
M +++L + G +++ +K V+ F + T IVG NG GK+ I + I F L
Sbjct: 1 MPYIEKLELKGFKSY-GNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVL 50
>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 = 34.3 bits (77), Expect = 0.51, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 4 LDQLHIMGIRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
+++L + G +++ +K V+ F + T IVG NG GK+ I + I F L
Sbjct: 4 IEKLELKGFKSY-GNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVL 50
>pdb|3OZX|A Chain A, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
pdb|3OZX|B Chain B, Crystal Structure Of Abce1 Of Sulfolubus Solfataricus
(-Fes Domain)
Length = 538
Score = 34.3 bits (77), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 865 TFRSKIESGQTRLNSHNEKLQSLQKQKNDIHSKQLTVQG 903
TFR E+G+ R+N L +QK++ D +S L+ QG
Sbjct: 489 TFRRDAETGRPRVNKIGSYLDRVQKERGDYYSMVLSTQG 527
>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 = 34.3 bits (77), Expect = 0.55, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 4 LDQLHIMGIRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFAL 51
+++L + G +++ +K V+ F + T IVG NG GK+ I + I F L
Sbjct: 4 IEKLELKGFKSY-GNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVL 50
>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 = 33.9 bits (76), Expect = 0.62, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 4 LDQLHIMGIRNFPADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFALTNEYPQGASSGK 63
L +L++ G ++F + ++ F +T IVG NG GK+ II+ IK+ + + + +
Sbjct: 3 LKKLYLKGFKSF--GRPSLIGFSDRVTAIVGPNGSGKSNIIDAIKWVFGEQSKKELRASE 60
Query: 64 NF 65
F
Sbjct: 61 KF 62
>pdb|1G29|1 Chain 1, Malk
pdb|1G29|2 Chain 2, Malk
Length = 372
Score = 33.1 bits (74), Expect = 1.2, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 12/71 (16%)
Query: 1245 RDHKALAETFSRNCGIFALDEPTTNLD----------IKNASDQKNFQLIVITHDEEFIE 1294
R AL R +F +DEP +NLD +K Q I +THD+ +E
Sbjct: 145 RQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQ--VE 202
Query: 1295 NLTAIDRAYVV 1305
+T DR V+
Sbjct: 203 AMTMGDRIAVM 213
>pdb|1Z7L|A Chain A, Crystal Structure Of Fragment Of Mouse
Ubiquitin-Activating Enzyme
pdb|1Z7L|B Chain B, Crystal Structure Of Fragment Of Mouse
Ubiquitin-Activating Enzyme
pdb|1Z7L|C Chain C, Crystal Structure Of Fragment Of Mouse
Ubiquitin-Activating Enzyme
Length = 276
Score = 31.2 bits (69), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 408 QYTPEEGEGLIKMSQTTIDKYLSDIKILERT 438
Q+ +E EGL K +++YL+D K +ERT
Sbjct: 31 QWARDEFEGLFKQPAENVNQYLTDSKFVERT 61
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 31.2 bits (69), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 3/96 (3%)
Query: 30 TLIVGENGCGKTTIIECIKFALTNEYPQGASSGKNFVHDPRIGKKDEASASSGKNF-VHD 88
T+I GCGKT + I ++PQG GK +I ++ + K F H
Sbjct: 30 TIICAPTGCGKTFVSLLICEHHLKKFPQG-QKGKVVFFANQIPVYEQQKSVFSKYFERHG 88
Query: 89 PRI-GKKDETHAIVKLQCTCENNDTVCVVRSLLLSN 123
R+ G T V ++ ENND + + +L++N
Sbjct: 89 YRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 124
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 30.8 bits (68), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 3/96 (3%)
Query: 30 TLIVGENGCGKTTIIECIKFALTNEYPQGASSGKNFVHDPRIGKKDEASASSGKNF-VHD 88
T+I GCGKT + I ++PQG GK +I ++ + K F H
Sbjct: 31 TIICAPTGCGKTFVSLLICEHHLKKFPQG-QKGKVVFFANQIPVYEQNKSVFSKYFERHG 89
Query: 89 PRI-GKKDETHAIVKLQCTCENNDTVCVVRSLLLSN 123
R+ G T V ++ ENND + + +L++N
Sbjct: 90 YRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 125
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 30.8 bits (68), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 3/96 (3%)
Query: 30 TLIVGENGCGKTTIIECIKFALTNEYPQGASSGKNFVHDPRIGKKDEASASSGKNF-VHD 88
T+I GCGKT + I ++PQG GK +I ++ + K F H
Sbjct: 22 TIICAPTGCGKTFVSLLICEHHLKKFPQG-QKGKVVFFANQIPVYEQNKSVFSKYFERHG 80
Query: 89 PRI-GKKDETHAIVKLQCTCENNDTVCVVRSLLLSN 123
R+ G T V ++ ENND + + +L++N
Sbjct: 81 YRVTGISGATAENVPVEQIVENNDIIILTPQILVNN 116
>pdb|2O5V|A Chain A, Recombination Mediator Recf
Length = 359
Score = 30.4 bits (67), Expect = 7.3, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 4 LDQLHIMGIRNF-PADKNRVVRFQRPLTLIVGENGCGKTTIIECIKFALTNE 54
L L + RN P N F +T I GENG GKT ++E ALT +
Sbjct: 6 LSALSTLNYRNLAPGTLN----FPEGVTGIYGENGAGKTNLLEAAYLALTGQ 53
>pdb|1NRJ|B Chain B, Signal Recognition Particle Receptor Beta-Subunit In
Complex With The Srx Domain From The Alpha-Subunit
Length = 218
Score = 30.0 bits (66), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 51/99 (51%), Gaps = 13/99 (13%)
Query: 415 EGLIKMSQTTID--KYLSDIKILERTFSDNENTKQAEINALIV-EKVEL-----ESKIKS 466
+GLI M +T+D K + + L S E++ + I+ LI K EL SKIK
Sbjct: 84 KGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKD 143
Query: 467 -----FKQQIEGNKKDLTNVITQINEVNQSQSTLQVLQT 500
++ IE KK L V +INE + +++TL VLQ+
Sbjct: 144 ALESEIQKVIERRKKSLNEVERKINEEDYAENTLDVLQS 182
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
0.315 0.131 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 38,785,443
Number of Sequences: 62578
Number of extensions: 1516587
Number of successful extensions: 5270
Number of sequences better than 100.0: 78
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 56
Number of HSP's that attempted gapping in prelim test: 5137
Number of HSP's gapped (non-prelim): 190
length of query: 1491
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1380
effective length of database: 8,027,179
effective search space: 11077507020
effective search space used: 11077507020
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: 58 (26.9 bits)