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= 013882
(434 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 155 bits (392), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 91/230 (39%), Positives = 129/230 (56%), Gaps = 14/230 (6%)
Query: 2 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSY 61
LV +FF V++ W WPNPV+L +E L VWDPR N D+ H MPIITPAYP NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTY 327
Query: 62 NVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDL 121
NVS ST VM+++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+ + A
Sbjct: 328 NVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQR 387
Query: 122 LAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAHCAFFMGLQRKP 176
L W G VES++R L +E++ + L Q P P E D K + +GL K
Sbjct: 388 LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFRTMWVIGLVFKK 445
Query: 177 GEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQI 221
E E D+ ++ F + +IN MF + M+I H++RKQ+
Sbjct: 446 TE-NSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHVKRKQL 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 155 bits (391), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 91/230 (39%), Positives = 129/230 (56%), Gaps = 14/230 (6%)
Query: 2 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSY 61
LV +FF V++ W WPNPV+L +E L VWDPR N D+ H MPIITPAYP NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTY 327
Query: 62 NVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDL 121
NVS ST VM+++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+ + A
Sbjct: 328 NVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQR 387
Query: 122 LAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAHCAFFMGLQRKP 176
L W G VES++R L +E++ + L Q P P E D K + +GL K
Sbjct: 388 LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFRTMWVIGLVFKK 445
Query: 177 GEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQI 221
E E D+ ++ F + +IN MF + M+I H++RKQ+
Sbjct: 446 TE-NSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHVKRKQL 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 135 bits (339), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 87/230 (37%), Positives = 125/230 (54%), Gaps = 14/230 (6%)
Query: 2 LVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSSY 61
LV +FF V++ W WPNPV+L +E L VWDPR N D+ H PIITPAYP NS+Y
Sbjct: 268 LVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPIITPAYPQQNSTY 327
Query: 62 NVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADDL 121
NVS ST V +++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+ + A
Sbjct: 328 NVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQR 387
Query: 122 LAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAHCAFFMGLQRKP 176
L W G VES++R L +E++ + L Q P P E D K + +GL K
Sbjct: 388 LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFRTXWVIGLVFKK 445
Query: 177 GEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQI 221
E E D+ ++ F + +IN F + +I H++RKQ+
Sbjct: 446 TE-NSENLSVDLTYDIQSFTDTVYRQAINSKXF-EVDXKIAAXHVKRKQL 493
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 119 bits (299), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 56/157 (35%), Positives = 95/157 (60%), Gaps = 2/157 (1%)
Query: 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 60
++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+ITPAYP M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADD 120
+N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL++ +D+
Sbjct: 314 HNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDE 373
Query: 121 L-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 156
L W G VES++R L + +E K+ HP+ +
Sbjct: 374 QHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>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 = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 56/157 (35%), Positives = 95/157 (60%), Gaps = 2/157 (1%)
Query: 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 60
++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+ITPAYP M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADD 120
+N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL++ +D+
Sbjct: 314 HNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDE 373
Query: 121 L-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 156
L W G VES++R L + +E K+ HP+ +
Sbjct: 374 QHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>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 = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 56/157 (35%), Positives = 95/157 (60%), Gaps = 2/157 (1%)
Query: 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 60
++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+ITPAYP M ++
Sbjct: 254 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 313
Query: 61 YNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADD 120
+N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL++ +D+
Sbjct: 314 HNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDE 373
Query: 121 L-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 156
L W G VES++R L + +E K+ HP+ +
Sbjct: 374 QHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 56/157 (35%), Positives = 95/157 (60%), Gaps = 2/157 (1%)
Query: 1 MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPIITPAYPCMNSS 60
++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+ITPAYP M ++
Sbjct: 250 VILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCAT 309
Query: 61 YNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQVDIVAANADD 120
+N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL++ +D+
Sbjct: 310 HNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDE 369
Query: 121 L-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 156
L W G VES++R L + +E K+ HP+ +
Sbjct: 370 QHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 405
>pdb|3SEJ|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SJP|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SLD|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLN|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
Length = 311
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 236 PRLASQQRSSENGNEYQTGSGLKRKKDPESVDQDGPEKRQSISPQKQDSLSPDHLAPSSV 295
P+L S Q S++ N+++TG + P V QDG Q+ + Q + PD+ S
Sbjct: 140 PKLGSVQFSTDTSNDFETGQ--NTRFTPVGVVQDGSTTHQN---EPQQWVLPDYSGRDSH 194
Query: 296 RSGTGSNVEPVIPDKRVL 313
V P P +++L
Sbjct: 195 NVHLAPAVAPTFPGEQLL 212
>pdb|2OBR|A Chain A, Crystal Structures Of P Domain Of Norovirus Va387
pdb|2OBS|A Chain A, Crystal Structures Of P Domain Of Norovirus Va387 In
Complex With Blood Group Trisaccharides Type A
pdb|2OBT|A Chain A, Crystal Structures Of P Domain Of Norovirus Va387 In
Complex With Blood Group Trisaccharides Type B
Length = 327
Score = 28.5 bits (62), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 236 PRLASQQRSSENGNEYQTGSGLKRKKDPESVDQDG----PEKRQSISPQKQDSLSPD-HL 290
P+L S Q +++ N+ QTG K P V QDG E +Q + P + HL
Sbjct: 148 PKLGSVQYTTDTNNDLQTGQ--NTKFTPVGVIQDGNNHQNEPQQWVLPNYSGRTGHNVHL 205
Query: 291 APSSVRSGTGSNVEPVIPDKRVL 313
AP+ V P P +++L
Sbjct: 206 APA---------VAPTFPGEQLL 219
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
0.318 0.134 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,935,185
Number of Sequences: 62578
Number of extensions: 459188
Number of successful extensions: 743
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 732
Number of HSP's gapped (non-prelim): 10
length of query: 434
length of database: 14,973,337
effective HSP length: 102
effective length of query: 332
effective length of database: 8,590,381
effective search space: 2852006492
effective search space used: 2852006492
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)