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= 029420
(193 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CJQ|A Chain A, Bovine Viral Diarrhea Virus Cp7-R12 Rna-Dependent Rna
Polymerase
Length = 720
Score = 33.5 bits (75), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 88 LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
L + ++ NW K +PV++ + E + L ++F KVR EW
Sbjct: 296 LAITKVMYNWVKQQPVVIPGY-EGKTPLFNIFNKVRKEW 333
>pdb|1S4F|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
pdb|1S4F|B Chain B, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
pdb|1S4F|C Chain C, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
pdb|1S4F|D Chain D, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 2 From Bovine Viral Diarrhea Virus (Bvdv)
Length = 601
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 88 LTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
L + ++ NW K +PV++ + E + L ++F KVR EW
Sbjct: 218 LAITKVMYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 255
>pdb|1S48|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 1 (Residues 71-679) From Bvdv
pdb|1S49|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase
Construct 1 (Residues 71-679) From Bovine Viral Diarrhea
Virus Complexed With Gtp
Length = 609
Score = 32.3 bits (72), Expect = 0.16, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 73 EIRMPSIRKSSVSEGLTVEGILENWSKIKPVIMEDWSENRDALVDLFGKVRDEW 126
E R I+ L + + NW K +PV++ + E + L ++F KVR EW
Sbjct: 211 EKRPRVIQYPEAKTRLAITKVXYNWVKQQPVVIPGY-EGKTPLFNIFDKVRKEW 263
>pdb|2QS0|A Chain A, Quinolinate Synthase From Pyrococcus Furiosus
Length = 323
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 40/93 (43%), Gaps = 20/93 (21%)
Query: 100 IKPVIMEDWSENRDALVDLFGKVR-----DEW-------MDKDLTTWIGANRFYPGIPDA 147
+ P + E+ D +V G +R DEW M L+ +FYP DA
Sbjct: 219 VHPECNPEVQEHADIIVSTGGMIRRACEWDEWVVFTEREMVYRLSKLYPNKKFYPAKEDA 278
Query: 148 LKFASSRIYIVTTKAVSQMLYYESLQELQYHLT 180
+ V KA++ YESL++++Y +T
Sbjct: 279 V--------CVGMKAITLQHVYESLRDMKYEVT 303
>pdb|3GM8|A Chain A, Crystal Structure Of A Beta-glycosidase From Bacteroides
Vulgatus
Length = 801
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 111 NRDALVDLFGKVRDEWMDKDLTTWIGANRFYPGI 144
N+ D +G DEW KD+T +I +R +P I
Sbjct: 355 NQPKAADDYGNYFDEWWQKDMTDFIKRDRNHPSI 388
>pdb|2BR2|A Chain A, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|C Chain C, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|E Chain E, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|G Chain G, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|I Chain I, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|K Chain K, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|M Chain M, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|O Chain O, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|S Chain S, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|U Chain U, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|W Chain W, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C38|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
Length = 275
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 3 DLYALDFDGVLCDSCGESSLSAVKAAKVRWPGLFDGVDSVIEDWIVDQMHILRPVV 58
D+Y LD+ G + D+C +S++A+ KV SV ++ +V ++ + PVV
Sbjct: 143 DVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVV 198
>pdb|2JE6|A Chain A, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 277
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 3 DLYALDFDGVLCDSCGESSLSAVKAAKVRWPGLFDGVDSVIEDWIVDQMHILRPVV 58
D+Y LD+ G + D+C +S++A+ KV SV ++ +V ++ + PVV
Sbjct: 145 DVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVV 200
>pdb|3BVG|A Chain A, Manipulating The Coupled Folding And Binding Process
Drives Affinity Maturation In A Protein-Protein Complex
Length = 237
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 94 LENWSKIKPVIM-EDWSEN-RDALVDLFGK---VRDEWMDKDLTTWIGANRFYPGI 144
L+N+ K+K ++ ED ++ +D +VD++G V + KD +TW G Y GI
Sbjct: 58 LKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFSSKDASTWHGKTCMYGGI 113
>pdb|3TQI|A Chain A, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|B Chain B, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|C Chain C, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
pdb|3TQI|D Chain D, Structure Of The Gmp Synthase (Guaa) From Coxiella
Burnetii
Length = 527
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 26/56 (46%)
Query: 105 MEDWSENRDALVDLFGKVRDEWMDKDLTTWIGANRFYPGIPDALKFASSRIYIVTT 160
+ D E R + F +V +E K W+G YP + ++ K + + +I+ T
Sbjct: 304 ISDPEEKRKIAGEQFIRVFEEQAKKLNVKWLGQGTIYPDVIESAKTKTGKGHIIKT 359
>pdb|3L7Z|A Chain A, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|D Chain D, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|G Chain G, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 271
Score = 27.3 bits (59), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 3 DLYALDFDGVLCDSCGESSLSAVKAAKV 30
D+Y LD+ G + D+C +S++A+ KV
Sbjct: 143 DVYVLDYGGNVLDACTLASVAALYNTKV 170
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 0.136 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,659,381
Number of Sequences: 62578
Number of extensions: 213388
Number of successful extensions: 543
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 535
Number of HSP's gapped (non-prelim): 23
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
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: 49 (23.5 bits)