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= 004802
(729 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 = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 71/292 (24%), Positives = 116/292 (39%), Gaps = 53/292 (18%)
Query: 98 DIDLTAFGGLNVEEALAN---DVCSVLEREDQNKAA------EFVVKDAQ---LIRAEVK 145
D +L AFG L AL N D+C +++ Q+ E + + + L RA +
Sbjct: 54 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIP 113
Query: 146 LVKC-------LVQNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYY 198
++K + DI FN + L +L D K ++L+K W
Sbjct: 114 IIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHWAK- 169
Query: 199 ESRILGAHHGLISTYALETLVLY-IFHL-----FHSSLNGPLAVLYKFLDYFS-KFD--- 248
+I + G +S+Y +VLY + H+ F + L PL K +D F FD
Sbjct: 170 RKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQ-EKIVDGFDVGFDDKL 228
Query: 249 --------WDSYCISLNGPVRISSL---PEVVVETPENSGGDLLLSSEFLKECVEQFSVP 297
+ S L+G R + P V T G +L + + ++
Sbjct: 229 EDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDG-------YLTKQEKGWTSA 281
Query: 298 SRGFDTNSRSFPPKH-LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 348
+ + + ++ L I DP + +NN+GR+VS YRIR F +R L
Sbjct: 282 TEHTGSADQIIKDRYILAIEDPFEISNNVGRTVSSSGLYRIRGEFMAASRLL 333
>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 = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 70/292 (23%), Positives = 116/292 (39%), Gaps = 53/292 (18%)
Query: 98 DIDLTAFGGLNVEEALAN---DVCSVLEREDQNKAA------EFVVKDAQ---LIRAEVK 145
D +L AFG L AL N D+C +++ Q+ E + + + L RA +
Sbjct: 82 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIP 141
Query: 146 LVKC-------LVQNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYY 198
++K + DI FN + L +L D K ++L+K W
Sbjct: 142 IIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHWAK- 197
Query: 199 ESRILGAHHGLISTYALETLVLY-IFHL-----FHSSLNGPLAVLYKFLDYFS-KFD--- 248
+I + G +S+Y +VLY + H+ F + L PL K +D F FD
Sbjct: 198 RKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQ-EKIVDGFDVGFDDKL 256
Query: 249 --------WDSYCISLNGPVRISSL---PEVVVETPENSGGDLLLSSEFLKECVEQFSVP 297
+ S L+G R + P V T G +L + + ++
Sbjct: 257 EDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDG-------YLTKQEKGWTSA 309
Query: 298 SRGFDTNSRSFPPKH-LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 348
+ + + ++ L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 310 TEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 361
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 70/292 (23%), Positives = 116/292 (39%), Gaps = 53/292 (18%)
Query: 98 DIDLTAFGGLNVEEALAN---DVCSVLEREDQNKAA------EFVVKDAQ---LIRAEVK 145
D +L AFG L AL N D+C +++ Q+ E + + + L RA +
Sbjct: 54 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIP 113
Query: 146 LVKC-------LVQNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYY 198
++K + DI FN + L +L D K ++L+K W
Sbjct: 114 IIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHWAK- 169
Query: 199 ESRILGAHHGLISTYALETLVLY-IFHL-----FHSSLNGPLAVLYKFLDYFS-KFD--- 248
+I + G +S+Y +VLY + H+ F + L PL K +D F FD
Sbjct: 170 RKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQ-EKIVDGFDVGFDDKL 228
Query: 249 --------WDSYCISLNGPVRISSL---PEVVVETPENSGGDLLLSSEFLKECVEQFSVP 297
+ S L+G R + P V T G +L + + ++
Sbjct: 229 EDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDG-------YLTKQEKGWTSA 281
Query: 298 SRGFDTNSRSFPPKH-LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 348
+ + + ++ L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 282 TEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 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 = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 70/292 (23%), Positives = 116/292 (39%), Gaps = 53/292 (18%)
Query: 98 DIDLTAFGGLNVEEALAN---DVCSVLEREDQNKAA------EFVVKDAQ---LIRAEVK 145
D +L AFG L AL N D+C +++ Q+ E + + + L RA +
Sbjct: 45 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIP 104
Query: 146 LVKC-------LVQNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYY 198
++K + DI FN + L +L D K ++L+K W
Sbjct: 105 IIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHWAK- 160
Query: 199 ESRILGAHHGLISTYALETLVLY-IFHL-----FHSSLNGPLAVLYKFLDYFS-KFD--- 248
+I + G +S+Y +VLY + H+ F + L PL K +D F FD
Sbjct: 161 RKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQ-EKIVDGFDVGFDDKL 219
Query: 249 --------WDSYCISLNGPVRISSL---PEVVVETPENSGGDLLLSSEFLKECVEQFSVP 297
+ S L+G R + P V T G +L + + ++
Sbjct: 220 EDIPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDG-------YLTKQEKGWTSA 272
Query: 298 SRGFDTNSRSFPPKH-LNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKL 348
+ + + ++ L I DP + ++N+GR+VS YRIR F +R L
Sbjct: 273 TEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLL 324
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 37.7 bits (86), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 40/183 (21%), Positives = 75/183 (40%), Gaps = 13/183 (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-EQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLVLYI 222
G+ + E +D G R ++LI + R+ H G + +++ LV
Sbjct: 142 NGIEAAKLIREWLDDTPG-----LRELVLIVKQFLHARRLNNVHTGGLGGFSIICLVFSF 196
Query: 223 FHL 225
H+
Sbjct: 197 LHM 199
>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 = 5.3, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 13/90 (14%)
Query: 487 VISNETSKCSSLSGEESKARHAPHLYFSSSTMGNGE------IR------NGNSEWKQQL 534
V + E+ K S L+ + +PH FS TMG+G+ I+ +G W ++
Sbjct: 715 VPAWESQKHSPLAVKYPLGMLSPHPRFSMHTMGDGKNSYMNYIKDHRVEVDGYKYWIMRV 774
Query: 535 NSGSAE-KNVTSGILPTHYKETGLILLNGQ 563
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
0.316 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,612,766
Number of Sequences: 62578
Number of extensions: 952946
Number of successful extensions: 2069
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2065
Number of HSP's gapped (non-prelim): 6
length of query: 729
length of database: 14,973,337
effective HSP length: 106
effective length of query: 623
effective length of database: 8,340,069
effective search space: 5195862987
effective search space used: 5195862987
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)