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= psy10458
(563 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PQ1|A Chain A, Crystal Structure Of Human Mitochondrial Poly(A)
Polymerase (Papd1)
pdb|3PQ1|B Chain B, Crystal Structure Of Human Mitochondrial Poly(A)
Polymerase (Papd1)
Length = 464
Score = 178 bits (451), Expect = 8e-45, Method: Compositional matrix adjust.
Identities = 118/370 (31%), Positives = 182/370 (49%), Gaps = 43/370 (11%)
Query: 131 ECLASCNTITQQMTTLHNITKMNDINTRLRFLVAYQVELALSGLFPLCAIFPFGSSVNNF 190
E L +I Q+ TL ++ + NT+LR+L +E + FP C + PFGSSVN F
Sbjct: 126 ELLCYAESIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDXAAAYFPDCIVRPFGSSVNTF 185
Query: 191 GKXXXXXXXXXXXXXXXXXXNDQCRLMFHCK---SSLGSERSQTLRHLETVGDLLQLFLP 247
GK + F + ++ SER T + L +G+
Sbjct: 186 GKLGCDLDXFLDLDETRNLSAHKISGNFLXEFQVKNVPSERIATQKILSVLGE------- 238
Query: 248 GCSQLFLPGCSQVKRILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEIDWR 307
C F PGC V++IL AR P+++++H S +C L+ N AL +ELLY++G +D R
Sbjct: 239 -CLDHFGPGCVGVQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIYGALDSR 297
Query: 308 VRPLVFTIKKWAKDINLTNPTPGRWITNFSLTLLVLFYLQ--SVKVLPPLKLLIDEASLK 365
VR LVF+++ WA+ +LT+ PG WITNFSLT V+F+LQ S +LP L L A +
Sbjct: 298 VRALVFSVRCWARAHSLTSSIPGAWITNFSLTXXVIFFLQRRSPPILPTLDSLKTLADAE 357
Query: 366 DRRISEDGVNCTFVRDITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISLYLG 425
D+ + E G NCTFVRD+++++ P Q+T++L LL FFE++ +
Sbjct: 358 DKCVIE-GNNCTFVRDLSRIK-----PSQNTETLELLLKEFFEYFGNFAXXXXXXXXX-- 409
Query: 426 SPIPKPEHGALYINNPLERGLNVSKNVSFEELERLKVEVRNASWTLESTANSNNKPSHTP 485
VS +L++ R ++W L+ ++PS +
Sbjct: 410 --------------------XXXXXXVSQSQLQKFVDLARESAWILQQ--EDTDRPSISS 447
Query: 486 SESWGLLELF 495
+ WGL+ L
Sbjct: 448 NRPWGLVSLL 457
>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 = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 72/235 (30%), Positives = 111/235 (47%), Gaps = 36/235 (15%)
Query: 266 ARVPIIKYNHDM-----SALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIKKWAK 320
AR+PIIK D ++ +CD+ N A++ LL + ++D R++P+V +K WAK
Sbjct: 138 ARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAK 197
Query: 321 DINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPLKLLIDEASLKDRRISEDGVNCTFVR 380
+ +P G ++++ L+VL+YL V + PP+ + + LK +I DG + F
Sbjct: 198 RKQINSPYFGT-LSSYGYVLMVLYYLIHV-IKPPVFPNLLLSPLKQEKIV-DGFDVGFD- 253
Query: 381 DITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISLYLGSP---IPKPEHG--- 434
KL+ P P Q+ SL +LL GFF FY+ Y F + + P + K E G
Sbjct: 254 --DKLEDIP--PSQNYSSLGSLLHGFFRFYA-YKFEPREKVVTFRRPDGYLTKQEKGWTS 308
Query: 435 ----------------ALYINNPLERGLNVSKNVSFEELERLKVEVRNASWTLES 473
L I +P E NV + VS L R++ E AS L S
Sbjct: 309 ATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNS 363
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 72/235 (30%), Positives = 111/235 (47%), Gaps = 36/235 (15%)
Query: 266 ARVPIIKYNHDM-----SALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIKKWAK 320
AR+PIIK D ++ +CD+ N A++ LL + ++D R++P+V +K WAK
Sbjct: 110 ARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAK 169
Query: 321 DINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPLKLLIDEASLKDRRISEDGVNCTFVR 380
+ +P G ++++ L+VL+YL V + PP+ + + LK +I DG + F
Sbjct: 170 RKQINSPYFGT-LSSYGYVLMVLYYLIHV-IKPPVFPNLLLSPLKQEKIV-DGFDVGFD- 225
Query: 381 DITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISLYLGSP---IPKPEHG--- 434
KL+ P P Q+ SL +LL GFF FY+ Y F + + P + K E G
Sbjct: 226 --DKLEDIP--PSQNYSSLGSLLHGFFRFYA-YKFEPREKVVTFRRPDGYLTKQEKGWTS 280
Query: 435 ----------------ALYINNPLERGLNVSKNVSFEELERLKVEVRNASWTLES 473
L I +P E NV + VS L R++ E AS L S
Sbjct: 281 ATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNS 335
>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 = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 72/235 (30%), Positives = 111/235 (47%), Gaps = 36/235 (15%)
Query: 266 ARVPIIKYNHDM-----SALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIKKWAK 320
AR+PIIK D ++ +CD+ N A++ LL + ++D R++P+V +K WAK
Sbjct: 101 ARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAK 160
Query: 321 DINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPLKLLIDEASLKDRRISEDGVNCTFVR 380
+ +P G ++++ L+VL+YL V + PP+ + + LK +I DG + F
Sbjct: 161 RKQINSPYFGT-LSSYGYVLMVLYYLIHV-IKPPVFPNLLLSPLKQEKIV-DGFDVGFD- 216
Query: 381 DITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISLYLGSP---IPKPEHG--- 434
KL+ P P Q+ SL +LL GFF FY+ Y F + + P + K E G
Sbjct: 217 --DKLEDIP--PSQNYSSLGSLLHGFFRFYA-YKFEPREKVVTFRRPDGYLTKQEKGWTS 271
Query: 435 ----------------ALYINNPLERGLNVSKNVSFEELERLKVEVRNASWTLES 473
L I +P E NV + VS L R++ E AS L S
Sbjct: 272 ATEHTGSADQIIKDRYILAIEDPFEISHNVGRTVSSSGLYRIRGEFMAASRLLNS 326
>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 = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 72/235 (30%), Positives = 111/235 (47%), Gaps = 36/235 (15%)
Query: 266 ARVPIIKYNHDM-----SALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIKKWAK 320
AR+PIIK D ++ +CD+ N A++ LL + ++D R++P+V +K WAK
Sbjct: 110 ARIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAK 169
Query: 321 DINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPLKLLIDEASLKDRRISEDGVNCTFVR 380
+ +P G ++++ L+VL+YL V + PP+ + + LK +I DG + F
Sbjct: 170 RKQINSPYFGT-LSSYGYVLMVLYYLIHV-IKPPVFPNLLLSPLKQEKIV-DGFDVGFD- 225
Query: 381 DITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISLYLGSP---IPKPEHG--- 434
KL+ P P Q+ SL +LL GFF FY+ Y F + + P + K E G
Sbjct: 226 --DKLEDIP--PSQNYSSLGSLLHGFFRFYA-YKFEPREKVVTFRRPDGYLTKQEKGWTS 280
Query: 435 ----------------ALYINNPLERGLNVSKNVSFEELERLKVEVRNASWTLES 473
L I +P E NV + VS L R++ E AS L S
Sbjct: 281 ATEHTGSADQIIKDRYILAIEDPFEISNNVGRTVSSSGLYRIRGEFMAASRLLNS 335
>pdb|3HJ1|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp
pdb|3HJ1|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp
Length = 387
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 35/171 (20%), Positives = 79/171 (46%), Gaps = 22/171 (12%)
Query: 262 RILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEI--DWRVRPLVFTIKKWA 319
R + AR+P++++ ++ + CD+S+ N+ + +++L ++ D+ + +K W
Sbjct: 111 RYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDF-YGAYIHLVKAWG 169
Query: 320 KDINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPL--------KLLIDEASLKDRRISE 371
K + P + +F++T + L LQ + +LP +L + +A + +
Sbjct: 170 KAREVIAPERSTF-NSFTVTTMALMVLQELGLLPVFSKPTGEFGELTVADAEMLLQEFKL 228
Query: 372 DGVNCTFVRDITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISL 422
+ + D KL +++ L F E+Y++YDF+ +SL
Sbjct: 229 PPIYDSLHDDDEKL----------GEAVFFCLQRFAEYYAKYDFSAGTVSL 269
>pdb|3HIY|A Chain A, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HIY|B Chain B, Minor Editosome-Associated Tutase 1 With Bound Utp And Mg
pdb|3HJ4|A Chain A, Minor Editosome-Associated Tutase 1
pdb|3HJ4|B Chain B, Minor Editosome-Associated Tutase 1
Length = 384
Score = 42.0 bits (97), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 35/171 (20%), Positives = 77/171 (45%), Gaps = 22/171 (12%)
Query: 262 RILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEI--DWRVRPLVFTIKKWA 319
R + AR+P++++ ++ + CD+S+ N+ + +++L ++ D+ + +K W
Sbjct: 108 RYIRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDF-YGAYIHLVKAWG 166
Query: 320 KDINLTNPTPGRWITNFSLTLLVLFYLQSVKVLPPL--------KLLIDEASLKDRRISE 371
K + P + +F++T L LQ + +LP +L + +A +
Sbjct: 167 KAREVIAPERSTF-NSFTVTTXALXVLQELGLLPVFSKPTGEFGELTVADAEXLLQEFKL 225
Query: 372 DGVNCTFVRDITKLQFHPSIPEQSTDSLTTLLFGFFEFYSQYDFNNQGISL 422
+ + D KL +++ L F E+Y++YDF+ +SL
Sbjct: 226 PPIYDSLHDDDEKL----------GEAVFFCLQRFAEYYAKYDFSAGTVSL 266
>pdb|2IKF|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Utp
pdb|2IKF|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Utp
pdb|2NOM|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Dutp
pdb|2NOM|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Dutp
pdb|2Q0C|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Ctp
pdb|2Q0C|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Ctp
pdb|2Q0D|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Atp
pdb|2Q0D|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Atp
pdb|2Q0E|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Gtp
pdb|2Q0E|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Gtp
pdb|2Q0F|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Utp And Ump
pdb|2Q0F|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Utp And Ump
pdb|2Q0G|A Chain A, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Upu
pdb|2Q0G|B Chain B, Terminal Uridylyl Transferase 4 From Trypanosoma Brucei
With Bound Upu
Length = 353
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 46/203 (22%), Positives = 81/203 (39%), Gaps = 50/203 (24%)
Query: 278 SALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIKKWAKDINLTNPTPGRWITNFS 337
A++ D++ + + LL + E + R L +IK+W+K L G IT++
Sbjct: 151 GAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYG 210
Query: 338 LTLLVLFYL---QSVKVLPPLKLLIDEASLKDRRISEDGVNCTFVRDITKLQ-FHPSIP- 392
L+V++YL ++ +PP + D+++++ P +P
Sbjct: 211 FNLMVVYYLLQRNHLQFVPPSTI-----------------------DVSRVEPLPPHLPL 247
Query: 393 EQSTD---SLTTLLFGFFEFY-SQYDFNNQGISLYLGSPIPKPE---------------- 432
E+ D L T + F F+ ++D + Q ISL K E
Sbjct: 248 EEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGE 307
Query: 433 --HGALYINNPLERGLNVSKNVS 453
H I +P E LNV +NV+
Sbjct: 308 KVHYQWCIEDPYELNLNVGRNVT 330
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 257 CSQVKRILGARVPIIKYNHDMSALECDLSMTNLTALYMAELLYLFGEIDWRVRPLVFTIK 316
++V+ + ARVPIIK+ S + +S + A+L+ + + +R LV +K
Sbjct: 109 ATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNGIEAAKLIREWLDDTPGLRELVLIVK 168
Query: 317 KWAKDINLTNPTPGRWITNFSLTLLVLFYLQ 347
++ L N G + FS+ LV +L
Sbjct: 169 QFLHARRLNNVHTGG-LGGFSIICLVFSFLH 198
>pdb|4IRY|B Chain B, Influenza A Virus Tail-loop Free Nucleoprotein At 2.8 A
Resolution
pdb|4IRY|A Chain A, Influenza A Virus Tail-loop Free Nucleoprotein At 2.8 A
Resolution
Length = 483
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 444 RGLNVSKNVSFEELERLKVEVRNASWTLE----------------STANSNNKPSHTPSE 487
RG+ ++ N + E +E +E+R+ W + ST N+ + S +E
Sbjct: 361 RGVQIASNENMETMESSTLELRSRYWAIRTRSGGNTNQQRAGGGGSTGNTEGRTSDMRTE 420
Query: 488 SWGLLELFKKQNLSEKAKSVF 508
L+E + +++S + + VF
Sbjct: 421 IIRLMESARPEDVSFQGRGVF 441
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 0.134 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,425,708
Number of Sequences: 62578
Number of extensions: 591796
Number of successful extensions: 1273
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1253
Number of HSP's gapped (non-prelim): 16
length of query: 563
length of database: 14,973,337
effective HSP length: 104
effective length of query: 459
effective length of database: 8,465,225
effective search space: 3885538275
effective search space used: 3885538275
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: 54 (25.4 bits)