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= 005149
(712 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FHX|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - H336n Mutant Bound
To Mgatp
Length = 349
Score = 36.6 bits (83), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%)
Query: 296 LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 331
L I DP + +NN+GR+VS YRIR F +R L
Sbjct: 298 LAIEDPFEISNNVGRTVSSSGLYRIRGEFMAASRLL 333
>pdb|4FH3|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity
pdb|4FH5|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgutp Bound
pdb|4FHP|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Cautp Bound
pdb|4FHV|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgctp Bound
pdb|4FHW|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mggtp Bound
pdb|4FHY|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mg 3'-Datp Bound
Length = 349
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 296 LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 331
L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 298 LAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 333
>pdb|4EP7|A Chain A, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
pdb|4EP7|B Chain B, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
Length = 340
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 296 LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 331
L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 289 LAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 324
>pdb|4E7X|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
Length = 405
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 296 LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 331
L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 326 LAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 361
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 41/182 (22%), Positives = 76/182 (41%), Gaps = 14/182 (7%)
Query: 47 QGIIAQVQPTVVSEERRKAVIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAFG 105
+ +A + P+ E R I ++ ++ + ++ FGS YLP DID
Sbjct: 26 KDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVVTS 85
Query: 106 GLNVEEALANDVCSVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLV--QNIVVDISFNQL 163
L +E+ N + +N A E V + +A V ++K + I + +SF +
Sbjct: 86 ELGGKESRNNLYSLASHLKKKNLATEVEV----VAKARVPIIKFVEPHSGIHIAVSFERT 141
Query: 164 GGLSTLCFL-EQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLVLYK 222
G+ + E +D G R ++LI + R+ H G + +++ LV +
Sbjct: 142 NGIEAAKLIREWLDDTPG-----LRELVLIVKQFLHARRLNNVHTGGLGGFSIICLV-FS 195
Query: 223 FL 224
FL
Sbjct: 196 FL 197
>pdb|3IWJ|A Chain A, Crystal Structure Of Aminoaldehyde Dehydrogenase 2 From
Pisum Sativum (Psamadh2)
pdb|3IWJ|B Chain B, Crystal Structure Of Aminoaldehyde Dehydrogenase 2 From
Pisum Sativum (Psamadh2)
Length = 503
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 65/150 (43%), Gaps = 36/150 (24%)
Query: 200 SRILGAHHGLISTYALET-----LVLYKFLDYFSKFDWDSY-CISLNGPVRISSLPEVVV 253
S+I+ A L+ +LE LV+++ +D +W + C NG + ++ ++
Sbjct: 244 SKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILH 303
Query: 254 ETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVS 313
E+ +++EFL V+ K++ I DPL+E LG VS
Sbjct: 304 ES---------IATEFLNRIVKWI----------------KNIKISDPLEEGCRLGPVVS 338
Query: 314 KGNFYRIRSAFTYGARKLGHIL----SQPE 339
+G + +I F A+ G + S+PE
Sbjct: 339 EGQYEKILK-FVSNAKSEGATILTGGSRPE 367
>pdb|3GQ7|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment
pdb|3GQ8|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In Complex With
2-(N-Cyclohexylamino)ethane Sulfonic Acid (Ches)
pdb|3GQ9|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In An Apo Form
pdb|3GQA|A Chain A, Crystal Structure Of The Bacteriophage Phi29 Gene Product
12 N- Terminal Fragment In Complex With Cobalt Ions
Length = 609
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 199 ESRILGAHHGLISTYALETLVLYKFLDYFSKFDWDSYCISLNGPVR 244
+SR G H+ ++S+Y + T YK F K +W+ SLNG ++
Sbjct: 554 QSRASGNHNLILSSYGINTTGSYKVNGGFEKINWE--LDSLNGRIK 597
>pdb|3SUC|A Chain A, Crystal Structure Of The Pre-Mature Bacteriophage Phi29
Gene Product 12
Length = 772
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 199 ESRILGAHHGLISTYALETLVLYKFLDYFSKFDWDSYCISLNGPVR 244
+SR G H+ ++S+Y + T YK F K +W+ SLNG ++
Sbjct: 554 QSRASGNHNLILSSYGINTTGSYKVNGGFEKINWE--LDSLNGRIK 597
>pdb|1TI2|A Chain A, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI2|C Chain C, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI2|E Chain E, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI2|G Chain G, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI2|I Chain I, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI2|K Chain K, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1TI4|A Chain A, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI4|C Chain C, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI4|E Chain E, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI4|G Chain G, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI4|I Chain I, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI4|K Chain K, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1TI6|A Chain A, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1TI6|C Chain C, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1TI6|E Chain E, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1TI6|G Chain G, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1TI6|I Chain I, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1TI6|K Chain K, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLD|M Chain M, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLD|O Chain O, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLD|Q Chain Q, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLD|S Chain S, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLD|U Chain U, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLD|W Chain W, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici
pdb|1VLE|M Chain M, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLE|O Chain O, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLE|Q Chain Q, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLE|S Chain S, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLE|U Chain U, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLE|W Chain W, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Pyrogallol
pdb|1VLF|M Chain M, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLF|O Chain O, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLF|Q Chain Q, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLF|S Chain S, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLF|U Chain U, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
pdb|1VLF|W Chain W, Crystal Structure Of Pyrogallol-Phloroglucinol
Transhydroxylase From Pelobacter Acidigallici Complexed
With Inhibitor 1,2,4,5-Tetrahydroxy-Benzene
Length = 875
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 13/90 (14%)
Query: 470 VISNETSKCSSLSGEESKARHAPHLYFSSSTMGNGE------IR------NGNSEWKQQL 517
V + E+ K S L+ + +PH FS TMG+G+ I+ +G W ++
Sbjct: 715 VPAWESQKHSPLAVKYPLGMLSPHPRFSMHTMGDGKNSYMNYIKDHRVEVDGYKYWIMRV 774
Query: 518 NSGSAE-KNVTSGILPTHYKETGLILLNGQ 546
NS AE + + +G L Y + G ++L Q
Sbjct: 775 NSIDAEARGIKNGDLIRAYNDRGSVILAAQ 804
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 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,130,658
Number of Sequences: 62578
Number of extensions: 933693
Number of successful extensions: 2017
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2013
Number of HSP's gapped (non-prelim): 9
length of query: 712
length of database: 14,973,337
effective HSP length: 106
effective length of query: 606
effective length of database: 8,340,069
effective search space: 5054081814
effective search space used: 5054081814
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: 55 (25.8 bits)