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= 038458
(347 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 55/243 (22%), Positives = 94/243 (38%), Gaps = 36/243 (14%)
Query: 11 WLKAEEITAELIARIQPDPFSEERRNAVAAYVRRLIIQCFP-CQVFTFGSVPLKTYLPDR 69
WL E + +A I P E RN + +R + Q +P + FGS YLP
Sbjct: 20 WLTFE--IKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGS 77
Query: 70 DID------LGAFSDDQTLKDTWAHLVRDMLENEEKNEHAEFRVKEVQYIQAEVKIIKCL 123
DID LG L +HL + L E + A+ RV +++++ I
Sbjct: 78 DIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVV-AKARVPIIKFVEPHSGI---- 132
Query: 124 VDNFVVDIAFNQLGGLCTLCFLDEVDHLINE---NHLFKRSIILIKAWCYYESRILGGHH 180
+ ++F + G+ E LI E + R ++LI + R+ H
Sbjct: 133 ----HIAVSFERTNGI-------EAAKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHT 181
Query: 181 GLISSYALVTLVLYIFHVFNGSFAGPLE-------VLYRFLEFFSK-FDWDNFCLSLWGP 232
G + ++++ LV H+ ++ +L F E + K F +D+ L
Sbjct: 182 GGLGGFSIICLVFSFLHMHPRIITNEIDPKDNLGVLLIEFFELYGKNFGYDDVALGSSDG 241
Query: 233 VPI 235
P+
Sbjct: 242 YPV 244
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 50/184 (27%), Positives = 77/184 (41%), Gaps = 23/184 (12%)
Query: 24 RIQPDPFSEERRNAVAAYVRRLIIQCFP-CQVFTFGSVPLKTYLPDRDIDLGAFSDDQTL 82
+I F E+R A +R + + P ++ FGS+ L + D+DL D +
Sbjct: 28 KISDKEFKEKR--AALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQ 85
Query: 83 KDTWAHLVRDMLENEEKNEHAEFRVKEVQYIQAEVKIIKCLVD-------NFVVDIAFNQ 135
DT A L+ E+ F K +Q +A + IIK D +F DI FN
Sbjct: 86 SDTIA------LQFYEELIAEGFEGKFLQ--RARIPIIKLTSDTKNGFGASFQCDIGFNN 137
Query: 136 LGGLCTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVL-Y 194
+ L L + K ++L+K W +I + G +SSY V +VL Y
Sbjct: 138 RLAIHNTLLLSSYTKL---DARLKPMVLLVKHWA-KRKQINSPYFGTLSSYGYVLMVLYY 193
Query: 195 IFHV 198
+ HV
Sbjct: 194 LIHV 197
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 50/184 (27%), Positives = 77/184 (41%), Gaps = 23/184 (12%)
Query: 24 RIQPDPFSEERRNAVAAYVRRLIIQCFP-CQVFTFGSVPLKTYLPDRDIDLGAFSDDQTL 82
+I F E+R A +R + + P ++ FGS+ L + D+DL D +
Sbjct: 28 KISDKEFKEKR--AALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQ 85
Query: 83 KDTWAHLVRDMLENEEKNEHAEFRVKEVQYIQAEVKIIKCLVD-------NFVVDIAFNQ 135
DT A L+ E+ F K +Q +A + IIK D +F DI FN
Sbjct: 86 SDTIA------LQFYEELIAEGFEGKFLQ--RARIPIIKLTSDTKNGFGASFQCDIGFNN 137
Query: 136 LGGLCTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVL-Y 194
+ L L + K ++L+K W +I + G +SSY V +VL Y
Sbjct: 138 RLAIHNTLLLSSYTKL---DARLKPMVLLVKHWA-KRKQINSPYFGTLSSYGYVLMVLYY 193
Query: 195 IFHV 198
+ HV
Sbjct: 194 LIHV 197
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 50/184 (27%), Positives = 77/184 (41%), Gaps = 23/184 (12%)
Query: 24 RIQPDPFSEERRNAVAAYVRRLIIQCFP-CQVFTFGSVPLKTYLPDRDIDLGAFSDDQTL 82
+I F E+R A +R + + P ++ FGS+ L + D+DL D +
Sbjct: 19 KISDKEFKEKR--AALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQ 76
Query: 83 KDTWAHLVRDMLENEEKNEHAEFRVKEVQYIQAEVKIIKCLVD-------NFVVDIAFNQ 135
DT A L+ E+ F K +Q +A + IIK D +F DI FN
Sbjct: 77 SDTIA------LQFYEELIAEGFEGKFLQ--RARIPIIKLTSDTKNGFGASFQCDIGFNN 128
Query: 136 LGGLCTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVL-Y 194
+ L L + K ++L+K W +I + G +SSY V +VL Y
Sbjct: 129 RLAIHNTLLLSSYTKL---DARLKPMVLLVKHWA-KRKQINSPYFGTLSSYGYVLMVLYY 184
Query: 195 IFHV 198
+ HV
Sbjct: 185 LIHV 188
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 50/184 (27%), Positives = 76/184 (41%), Gaps = 23/184 (12%)
Query: 24 RIQPDPFSEERRNAVAAYVRRLIIQCFP-CQVFTFGSVPLKTYLPDRDIDLGAFSDDQTL 82
+I F E+R A +R + + P ++ FGS+ L + D+DL D +
Sbjct: 56 KISDKEFKEKR--AALDTLRLCLKRISPDAELVAFGSLESGLALKNSDMDLCVLMDSRVQ 113
Query: 83 KDTWAHLVRDMLENEEKNEHAEFRVKEVQYIQAEVKIIKCLVD-------NFVVDIAFNQ 135
DT A + L E F K +Q +A + IIK D +F DI FN
Sbjct: 114 SDTIALQFYEELIAE------GFEGKFLQ--RARIPIIKLTSDTKNGFGASFQCDIGFNN 165
Query: 136 LGGLCTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVL-Y 194
+ L L + K ++L+K W +I + G +SSY V +VL Y
Sbjct: 166 RLAIHNTLLLSSYTKL---DARLKPMVLLVKHWA-KRKQINSPYFGTLSSYGYVLMVLYY 221
Query: 195 IFHV 198
+ HV
Sbjct: 222 LIHV 225
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 47/208 (22%), Positives = 82/208 (39%), Gaps = 36/208 (17%)
Query: 46 IIQCFPCQVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDMLENEEKNEHAEF 105
+I+ ++FTFGS L + DID + + + D L+ +E+
Sbjct: 89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEE------ 142
Query: 106 RVKEVQYIQ-AEVKIIKCLVDNFVVDIAFNQLG-----------------GLCTLCF--- 144
VK+++ ++ A V +IK D +DI F +L L C
Sbjct: 143 -VKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSL 201
Query: 145 -----LDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVF 199
DE+ HL+ F+ ++ IK W + I G + + LV ++
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHN-IYSNILGFLGGVSWAXLVARTCQLY 260
Query: 200 NGSFAGPLEVLYRFLEFFSKFDWDNFCL 227
+ A L +++F FSK++W N L
Sbjct: 261 PNAIASTL--VHKFFLVFSKWEWPNPVL 286
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 46/208 (22%), Positives = 81/208 (38%), Gaps = 36/208 (17%)
Query: 46 IIQCFPCQVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDMLENEEKNEHAEF 105
+I+ ++FTFGS L + DID + + + D L+ +E+
Sbjct: 89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEE------ 142
Query: 106 RVKEVQYIQ-AEVKIIKCLVDNFVVDIAFNQLG-------------------------GL 139
VK+++ ++ A V +IK D +DI F +L L
Sbjct: 143 -VKDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSL 201
Query: 140 CTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVF 199
DE+ HL+ F+ ++ IK W + I G + + LV ++
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHN-IYSNILGFLGGVSWAMLVARTCQLY 260
Query: 200 NGSFAGPLEVLYRFLEFFSKFDWDNFCL 227
+ A L +++F FSK++W N L
Sbjct: 261 PNAIASTL--VHKFFLVFSKWEWPNPVL 286
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 46/208 (22%), Positives = 81/208 (38%), Gaps = 36/208 (17%)
Query: 46 IIQCFPCQVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDMLENEEKNEHAEF 105
+I+ ++FTFGS L + DID + + + D L+ +E+
Sbjct: 89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEE------ 142
Query: 106 RVKEVQYIQ-AEVKIIKCLVDNFVVDIAFNQLG-------------------------GL 139
VK+++ ++ A V +IK D +DI F +L L
Sbjct: 143 -VKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRXIRSL 201
Query: 140 CTLCFLDEVDHLINENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVF 199
DE+ HL+ F+ ++ IK W + I G + + LV ++
Sbjct: 202 NGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHN-IYSNILGFLGGVSWAMLVARTCQLY 260
Query: 200 NGSFAGPLEVLYRFLEFFSKFDWDNFCL 227
+ A L +++F FSK++W N L
Sbjct: 261 PNAIASTL--VHKFFLVFSKWEWPNPVL 286
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 44/206 (21%), Positives = 81/206 (39%), Gaps = 31/206 (15%)
Query: 53 QVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDML-ENEEKNEHA-------- 103
++FT+GS L + P DID ++ + + +L E +E +E A
Sbjct: 79 KIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVP 138
Query: 104 ----EFRVKEVQYI-----QAEVKIIKCLVD-NFVVDIAFNQLGGLCTLCFLDEVDHLIN 153
+F + I Q +V + L D N + ++ L L DE+ L+
Sbjct: 139 IIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVP 198
Query: 154 ENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVFNGSFAGPLEVLYRF 213
+ ++F+ ++ IK W + + G A LV I ++ + + +L RF
Sbjct: 199 KPNVFRIALRAIKLWAQRRA-VYANIFGFPGGVAWAMLVARICQLYPNACSAV--ILNRF 255
Query: 214 LEFFSKFDWDNFCLSLWGPVPISLLP 239
S+++W P P+ L P
Sbjct: 256 FIILSEWNW---------PQPVILKP 272
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 44/206 (21%), Positives = 81/206 (39%), Gaps = 31/206 (15%)
Query: 53 QVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDML-ENEEKNEHA-------- 103
++FT+GS L + P DID ++ + + +L E +E +E A
Sbjct: 83 KIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVP 142
Query: 104 ----EFRVKEVQYI-----QAEVKIIKCLVD-NFVVDIAFNQLGGLCTLCFLDEVDHLIN 153
+F + I Q +V + L D N + ++ L L DE+ L+
Sbjct: 143 IIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVP 202
Query: 154 ENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVFNGSFAGPLEVLYRF 213
+ ++F+ ++ IK W + + G A LV I ++ + + +L RF
Sbjct: 203 KPNVFRIALRAIKLWAQRRA-VYANIFGFPGGVAWAMLVARICQLYPNACSAV--ILNRF 259
Query: 214 LEFFSKFDWDNFCLSLWGPVPISLLP 239
S+++W P P+ L P
Sbjct: 260 FIILSEWNW---------PQPVILKP 276
>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
Length = 537
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 44/206 (21%), Positives = 81/206 (39%), Gaps = 31/206 (15%)
Query: 53 QVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDML-ENEEKNEHA-------- 103
++FT+GS L + P DID ++ + + +L E +E +E A
Sbjct: 83 KIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVP 142
Query: 104 ----EFRVKEVQYI-----QAEVKIIKCLVD-NFVVDIAFNQLGGLCTLCFLDEVDHLIN 153
+F + I Q +V + L D N + ++ L L DE+ L+
Sbjct: 143 IIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVP 202
Query: 154 ENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVFNGSFAGPLEVLYRF 213
+ ++F+ ++ IK W + + G A LV I ++ + + +L RF
Sbjct: 203 KPNVFRIALRAIKLWAQRRA-VYANIFGFPGGVAWAMLVARICQLYPNACSAV--ILNRF 259
Query: 214 LEFFSKFDWDNFCLSLWGPVPISLLP 239
S+++W P P+ L P
Sbjct: 260 FIILSEWNW---------PQPVILKP 276
>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
Length = 546
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 44/206 (21%), Positives = 81/206 (39%), Gaps = 31/206 (15%)
Query: 53 QVFTFGSVPLKTYLPDRDIDLGAFSDDQTLKDTWAHLVRDML-ENEEKNEHA-------- 103
++FT+GS L + P DID ++ + + +L E +E +E A
Sbjct: 83 KIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVP 142
Query: 104 ----EFRVKEVQYI-----QAEVKIIKCLVD-NFVVDIAFNQLGGLCTLCFLDEVDHLIN 153
+F + I Q +V + L D N + ++ L L DE+ L+
Sbjct: 143 IIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVP 202
Query: 154 ENHLFKRSIILIKAWCYYESRILGGHHGLISSYALVTLVLYIFHVFNGSFAGPLEVLYRF 213
+ ++F+ ++ IK W + + G A LV I ++ + + +L RF
Sbjct: 203 KPNVFRIALRAIKLWAQRRA-VYANIFGFPGGVAWAMLVARICQLYPNACSAV--ILNRF 259
Query: 214 LEFFSKFDWDNFCLSLWGPVPISLLP 239
S+++W P P+ L P
Sbjct: 260 FIILSEWNW---------PQPVILKP 276
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
0.325 0.143 0.447
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,549,508
Number of Sequences: 62578
Number of extensions: 430544
Number of successful extensions: 1194
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1180
Number of HSP's gapped (non-prelim): 20
length of query: 347
length of database: 14,973,337
effective HSP length: 100
effective length of query: 247
effective length of database: 8,715,537
effective search space: 2152737639
effective search space used: 2152737639
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)