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= 010247
(514 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 90/346 (26%), Positives = 141/346 (40%), Gaps = 65/346 (18%)
Query: 182 LLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDA 241
L RKDL + +ID A +L +G +V +H+AD T +++PG+ D +
Sbjct: 530 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEG 589
Query: 242 MKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIK 301
RGTSV+L M P L + SL+ A +V L +I + S+I+
Sbjct: 590 AARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIR 649
Query: 302 PTYMLTYESATXXXXXXXXXXXXXKILSEAAALRL-----QWRLQQGAIDTATLETRI-- 354
+YE A + A L+L Q RL+ GA++ A+ E ++
Sbjct: 650 SREAFSYEQAQLRIDDKTQNDELT--MGMRALLKLSVKLKQKRLEAGALNLASPEVKVHM 707
Query: 355 --KVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIA--TYGSFNNLALPYR--GQ 408
+ ++P + E I L + LV E M+L ++A Y +F A+ R
Sbjct: 708 DSETSDPNEVE-IKKLLATNS------LVEEFMLLANISVARKIYDAFPQTAMLRRHAAP 760
Query: 409 PQSNIDV------------------SAFAHL------PEGPVRSSAIVKIMRAAAI---- 440
P +N ++ A A PE P ++ +V+IM +
Sbjct: 761 PSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNT-LVRIMSTRCMMAAQ 819
Query: 441 ----------DFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVG 476
DF RH L + Y FTSPIRRY D++AH Q+
Sbjct: 820 YFYSGAYSYPDF----RHYGLAVDIYTHFTSPIRRYCDVVAHRQLA 861
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 90/346 (26%), Positives = 141/346 (40%), Gaps = 65/346 (18%)
Query: 182 LLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDA 241
L RKDL + +ID A +L +G +V +H+AD T +++PG+ D +
Sbjct: 504 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEG 563
Query: 242 MKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIK 301
RGTSV+L M P L + SL+ A +V L +I + S+I+
Sbjct: 564 AARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIR 623
Query: 302 PTYMLTYESATXXXXXXXXXXXXXKILSEAAALRL-----QWRLQQGAIDTATLETRI-- 354
+YE A + A L+L Q RL+ GA++ A+ E ++
Sbjct: 624 SREAFSYEQAQLRIDDKTQNDELT--MGMRALLKLSVKLKQKRLEAGALNLASPEVKVHM 681
Query: 355 --KVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIA--TYGSFNNLALPYR--GQ 408
+ ++P + E I L + LV E M+L ++A Y +F A+ R
Sbjct: 682 DSETSDPNEVE-IKKLLATNS------LVEEFMLLANISVARKIYDAFPQTAMLRRHAAP 734
Query: 409 PQSNIDV------------------SAFAHL------PEGPVRSSAIVKIMRAAAI---- 440
P +N ++ A A PE P ++ +V+IM +
Sbjct: 735 PSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNT-LVRIMSTRCMMAAQ 793
Query: 441 ----------DFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVG 476
DF RH L + Y FTSPIRRY D++AH Q+
Sbjct: 794 YFYSGAYSYPDF----RHYGLAVDIYTHFTSPIRRYCDVVAHRQLA 835
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|B Chain B, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|C Chain C, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7F|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Hexagonal Crystal Form.
Northeast Structural Genomics Target Drr63
Length = 469
Score = 75.9 bits (185), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 80/295 (27%), Positives = 119/295 (40%), Gaps = 23/295 (7%)
Query: 184 NRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMK 243
R DLTHL +AID L G ++++HVAD + P S D +A
Sbjct: 80 ERLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARA 139
Query: 244 RGTSVFLPTATYPMFPEKL-AMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKP 302
RG +++LP T P++L A G+ L EV A+++ + L DG+ V + +K
Sbjct: 140 RGATLYLPDRTIGXLPDELVAKAGLGLH--EVSPALSICLDLDPDGNAEAVDVLLTRVK- 196
Query: 303 TYMLTYESATXXXXXXXXXXXXXKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDP 362
L Y+ A L+ A+ + +GA+ E R+K
Sbjct: 197 VQRLAYQEAQARLEAGEEPFVTLARLARASRRLRE---GEGALSIDLPEVRVKADE---- 249
Query: 363 EPIINLYVEDQADPAMR-LVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVSAFAHL 421
V P R +V E L G A + N + LP+ Q +V+ L
Sbjct: 250 ---TGASVFPLPKPEXRTVVQECXTLAGWGTAIFADDNEIPLPFATQDYPTREVAGDT-L 305
Query: 422 PEGPVRSSAIVKIMRAAAIDFR-KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475
P R + + F+ P H GL Y Q TSP RRY+DL+ H Q+
Sbjct: 306 PAXWARRKTLARTR------FQPSPGPHHGXGLDLYAQATSPXRRYLDLVVHQQL 354
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 69.7 bits (169), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 84/341 (24%), Positives = 133/341 (39%), Gaps = 55/341 (16%)
Query: 182 LLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDA 241
L RKDL + +ID A +L +G +V +H+AD T +++PG+ D +
Sbjct: 287 LTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEG 346
Query: 242 MKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIK 301
RGTSV+L P L + SL+ A +V L +I + S+I+
Sbjct: 347 AARGTSVYLVDKRIDXLPXLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFXKSVIR 406
Query: 302 PTYMLTYESATXXXXXXXXXXXXXK----ILSEAAALRLQWRLQQGAIDTATLETRI--- 354
+YE A +L + L+ Q RL+ GA++ A+ E ++
Sbjct: 407 SREAFSYEQAQLRIDDKTQNDELTXGXRALLKLSVKLK-QKRLEAGALNLASPEVKVHXD 465
Query: 355 -KVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIA--TYGSFNNLALPYR--GQP 409
+ ++P + E I L + LV E +L ++A Y +F A R P
Sbjct: 466 SETSDPNEVE-IKKLLATNS------LVEEFXLLANISVARKIYDAFPQTAXLRRHAAPP 518
Query: 410 QSNIDV------------------SAFAHL------PEGP----------VRSSAIVKIM 435
+N ++ A A PE P R +
Sbjct: 519 STNFEILNEXLNTRKNXSISLESSKALADSLDRCVDPEDPYFNTLVRIXSTRCXXAAQYF 578
Query: 436 RAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVG 476
+ A + RH L + Y FTSPIRRY D++AH Q+
Sbjct: 579 YSGAYSY-PDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLA 618
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 63.2 bits (152), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 56/113 (49%)
Query: 180 DNLLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDK 239
D L R+DLT L ID A L D ++++ + +ADPT +I GS DK
Sbjct: 204 DEGLVREDLTALDFVTIDSASTEDMNDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 263
Query: 240 DAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAE 292
A R + +LP PM P +L+ + SLR EV + + L +DG+I +
Sbjct: 264 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIED 316
Score = 35.0 bits (79), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 444 KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVGLQAAAWVSVGAQIGDEVEVKVEE 499
+P H LGL Y +TSPIR+Y D++ H L+A + DE+ V++ E
Sbjct: 500 EPGPHFGLGLEAYATWTSPIRKYGDMINHRL--LKAVIKGETATRPQDEITVQMAE 553
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 63.2 bits (152), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 56/113 (49%)
Query: 180 DNLLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDK 239
D L R+DLT L ID A L D ++++ + +ADPT +I GS DK
Sbjct: 203 DEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 262
Query: 240 DAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAE 292
A R + +LP PM P +L+ + SLR EV + + L +DG+I +
Sbjct: 263 AAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIED 315
Score = 35.0 bits (79), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 444 KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVGLQAAAWVSVGAQIGDEVEVKVEE 499
+P H LGL Y +TSPIR+Y D++ H L+A + DE+ V++ E
Sbjct: 499 EPGPHFGLGLEAYATWTSPIRKYGDMINHRL--LKAVIKGETATRPQDEITVQMAE 552
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii
pdb|2ID0|B Chain B, Escherichia Coli Rnase Ii
pdb|2ID0|C Chain C, Escherichia Coli Rnase Ii
pdb|2ID0|D Chain D, Escherichia Coli Rnase Ii
Length = 644
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 55/113 (48%)
Query: 180 DNLLNRKDLTHLKVYAIDVXXXXXXXXXXSAMRLQDGRIKVYIHVADPTKYIEPGSLSDK 239
D L R+DLT L ID A L D ++++ + +ADPT +I GS DK
Sbjct: 184 DEGLVREDLTALDFVTIDSASTEDXDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDK 243
Query: 240 DAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAE 292
A R + +LP P P +L+ + SLR EV + L +DG+I +
Sbjct: 244 AAKIRAFTNYLPGFNIPXLPRELSDDLCSLRANEVRPVLACRXTLSADGTIED 296
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 444 KPVRHGVLGLPGYVQFTSPIRRYMDLLAH 472
+P H LGL Y +TSPIR+Y D + H
Sbjct: 480 EPGPHFGLGLEAYATWTSPIRKYGDXINH 508
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
0.320 0.134 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,674,356
Number of Sequences: 62578
Number of extensions: 515944
Number of successful extensions: 1125
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1108
Number of HSP's gapped (non-prelim): 16
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)