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= 006807
(630 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 130 bits (326), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 73/217 (33%), Positives = 117/217 (53%), Gaps = 10/217 (4%)
Query: 414 PDARLYLYGSCANSFGVSKSDIDVCLAINDSEINKSEVLLKLADILQSDNLQNVQALTRA 473
PDA L +GS + + SD+D+C+ + DS + + L+ + L ++ + + L RA
Sbjct: 81 PDAELVAFGSLESGLALKNSDMDLCVLM-DSRVQSDTIALQFYEELIAEGFEG-KFLQRA 138
Query: 474 RVPIVKLMDPV-----TGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWAKS 528
R+PI+KL CDI NN LA+ NT LL Y ++D RL+ + +VKHWAK
Sbjct: 139 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 198
Query: 529 RGVNVTYQGTLSSYAYVLMCIHFL-QQRRPAILPCLQGMEKTYSVTVDDIECAYFDQVDK 587
+ +N Y GTLSSY YVLM +++L +P + P L VD + + D+++
Sbjct: 199 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 258
Query: 588 LHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISVR 624
+ S+N S+G L+ FF ++AY + V++ R
Sbjct: 259 IP--PSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFR 293
>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 = 129 bits (325), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 73/217 (33%), Positives = 117/217 (53%), Gaps = 10/217 (4%)
Query: 414 PDARLYLYGSCANSFGVSKSDIDVCLAINDSEINKSEVLLKLADILQSDNLQNVQALTRA 473
PDA L +GS + + SD+D+C+ + DS + + L+ + L ++ + + L RA
Sbjct: 53 PDAELVAFGSLESGLALKNSDMDLCVLM-DSRVQSDTIALQFYEELIAEGFEG-KFLQRA 110
Query: 474 RVPIVKLMDPV-----TGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWAKS 528
R+PI+KL CDI NN LA+ NT LL Y ++D RL+ + +VKHWAK
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 170
Query: 529 RGVNVTYQGTLSSYAYVLMCIHFL-QQRRPAILPCLQGMEKTYSVTVDDIECAYFDQVDK 587
+ +N Y GTLSSY YVLM +++L +P + P L VD + + D+++
Sbjct: 171 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 230
Query: 588 LHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISVR 624
+ S+N S+G L+ FF ++AY + V++ R
Sbjct: 231 IP--PSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFR 265
>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 = 129 bits (325), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 73/217 (33%), Positives = 117/217 (53%), Gaps = 10/217 (4%)
Query: 414 PDARLYLYGSCANSFGVSKSDIDVCLAINDSEINKSEVLLKLADILQSDNLQNVQALTRA 473
PDA L +GS + + SD+D+C+ + DS + + L+ + L ++ + + L RA
Sbjct: 53 PDAELVAFGSLESGLALKNSDMDLCVLM-DSRVQSDTIALQFYEELIAEGFEG-KFLQRA 110
Query: 474 RVPIVKLMDPV-----TGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWAKS 528
R+PI+KL CDI NN LA+ NT LL Y ++D RL+ + +VKHWAK
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 170
Query: 529 RGVNVTYQGTLSSYAYVLMCIHFL-QQRRPAILPCLQGMEKTYSVTVDDIECAYFDQVDK 587
+ +N Y GTLSSY YVLM +++L +P + P L VD + + D+++
Sbjct: 171 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 230
Query: 588 LHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISVR 624
+ S+N S+G L+ FF ++AY + V++ R
Sbjct: 231 IP--PSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFR 265
>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 = 129 bits (323), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 73/217 (33%), Positives = 117/217 (53%), Gaps = 10/217 (4%)
Query: 414 PDARLYLYGSCANSFGVSKSDIDVCLAINDSEINKSEVLLKLADILQSDNLQNVQALTRA 473
PDA L +GS + + SD+D+C+ + DS + + L+ + L ++ + + L RA
Sbjct: 44 PDAELVAFGSLESGLALKNSDMDLCVLM-DSRVQSDTIALQFYEELIAEGFEG-KFLQRA 101
Query: 474 RVPIVKLMDPV-----TGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWAKS 528
R+PI+KL CDI NN LA+ NT LL Y ++D RL+ + +VKHWAK
Sbjct: 102 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 161
Query: 529 RGVNVTYQGTLSSYAYVLMCIHFL-QQRRPAILPCLQGMEKTYSVTVDDIECAYFDQVDK 587
+ +N Y GTLSSY YVLM +++L +P + P L VD + + D+++
Sbjct: 162 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 221
Query: 588 LHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISVR 624
+ S+N S+G L+ FF ++AY + V++ R
Sbjct: 222 IP--PSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFR 256
>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 = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 40/149 (26%), Positives = 77/149 (51%), Gaps = 7/149 (4%)
Query: 467 VQALTRARVPIVKLMDPVTGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWA 526
VQ + AR P+V+ +G C + NN +A+ +++LL Y +D R++ L F V+ WA
Sbjct: 250 VQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWA 309
Query: 527 KSRGVNVTYQGT-LSSYAYVLMCIHFLQQRRPAILPCLQGMEKTY----SVTVDDIECAY 581
++ + + G +++++ I FLQ+R P ILP L ++ ++ C +
Sbjct: 310 RAHSLTSSIPGAWITNFSLTXXVIFFLQRRSPPILPTLDSLKTLADAEDKCVIEGNNCTF 369
Query: 582 FDQVDKLHGFGSRNKESIGRLVWAFFNYW 610
+ ++ S+N E++ L+ FF Y+
Sbjct: 370 VRDLSRIK--PSQNTETLELLLKEFFEYF 396
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 46/152 (30%), Positives = 77/152 (50%), Gaps = 8/152 (5%)
Query: 413 WPDARLYLYGSCANSFGVSKSDIDVCLAINDSEINKSEV---LLKLADILQSDNLQN-VQ 468
WPDA L+++GS + + SDID + SE+ E L LA L+ NL V+
Sbjct: 57 WPDADLHVFGSYSTDLYLPGSDIDCVVT---SELGGKESRNNLYSLASHLKKKNLATEVE 113
Query: 469 ALTRARVPIVKLMDPVTGISCDICINNLLAVVNTKLLRDYAQIDVRLQQLAFIVKHWAKS 528
+ +ARVPI+K ++P +GI + + KL+R++ L++L IVK + +
Sbjct: 114 VVAKARVPIIKFVEPHSGIHIAVSFERTNGIEAAKLIREWLDDTPGLRELVLIVKQFLHA 173
Query: 529 RGVNVTYQGTLSSYAYVLMCIHFLQQRRPAIL 560
R +N + G L ++ + + FL P I+
Sbjct: 174 RRLNNVHTGGLGGFSIICLVFSFLHM-HPRII 204
>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 = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 58/227 (25%), Positives = 101/227 (44%), Gaps = 25/227 (11%)
Query: 416 ARLYLYGSCANSFGVSKSDIDVCLAIN------------DSEINKSEVLLKLADILQSDN 463
A + L+GS + F SD D+ L D + NK + + +
Sbjct: 49 AHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGMERVDEQNNKR--MTRFGKEASAMG 106
Query: 464 LQNVQALTRARVPIVKLMDPVTGISCDICINNLLAVVNTKLLRDYAQIDVRLQ-QLAFIV 522
+++V+ + RAR+P+V+ D VTGI CD+ I N+ V N+K+L Q+ +V
Sbjct: 107 MEDVRYI-RARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLV 165
Query: 523 KHWAKSRGVNVTYQGTLSSYAYVLMCIHFLQQRRPAILPCLQGMEKTY-SVTVDDIECAY 581
K W K+R V + T +S+ M + LQ+ +LP + +TV D E
Sbjct: 166 KAWGKAREVIAPERSTFNSFTVTTMALMVLQEL--GLLPVFSKPTGEFGELTVADAEMLL 223
Query: 582 FD-----QVDKLHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISV 623
+ D LH + E++ + F Y+A +D+++ +S+
Sbjct: 224 QEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYA-KYDFSAGTVSL 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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 57/227 (25%), Positives = 98/227 (43%), Gaps = 25/227 (11%)
Query: 416 ARLYLYGSCANSFGVSKSDIDVCLAIN------------DSEINKSEVLLKLADILQSDN 463
A + L+GS + F SD D+ L D + NK + +
Sbjct: 46 AHVELFGSHVSGFCTPHSDADISLTYRNFSPWLQGXERVDEQNNKRXT--RFGKEASAXG 103
Query: 464 LQNVQALTRARVPIVKLMDPVTGISCDICINNLLAVVNTKLLRDYAQIDVRLQ-QLAFIV 522
++V+ + RAR+P+V+ D VTGI CD+ I N+ V N+K+L Q+ +V
Sbjct: 104 XEDVRYI-RARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHLV 162
Query: 523 KHWAKSRGVNVTYQGTLSSYAYVLMCIHFLQQRRPAILPCLQGMEKTY-SVTVDDIECAY 581
K W K+R V + T +S+ + LQ+ +LP + +TV D E
Sbjct: 163 KAWGKAREVIAPERSTFNSFTVTTXALXVLQEL--GLLPVFSKPTGEFGELTVADAEXLL 220
Query: 582 FD-----QVDKLHGFGSRNKESIGRLVWAFFNYWAYGHDYASNVISV 623
+ D LH + E++ + F Y+A +D+++ +S+
Sbjct: 221 QEFKLPPIYDSLHDDDEKLGEAVFFCLQRFAEYYA-KYDFSAGTVSL 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 = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 83/160 (51%), Gaps = 20/160 (12%)
Query: 414 PDARLYLYGSCANSFGVSK--SDID-VCLAINDSEINK-------------SEVLLKLAD 457
P RLY +GS +GV + SD+D V L D E K +++L KLA
Sbjct: 65 PLMRLYTFGSTV-VYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLAR 123
Query: 458 ILQSDNLQ-NVQALTRARVPIVKLMDPVTGISCDICINNLLAVVNTKLLRDYAQIDVRLQ 516
+++ +L NV+ + R RVP+V++ + DI V N+ LLR Y + + +
Sbjct: 124 VIRQKHLSWNVEEVRRTRVPVVRVKGG-GAVDFDITAYRRNGVRNSALLRAYFEQNPPCR 182
Query: 517 QLAFIVKHWAKSRGVNVTY-QGTLSSYAYVLMCIHFLQQR 555
L+ +K W+K G+N + G+++SY + LM +++L QR
Sbjct: 183 WLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQR 222
>pdb|2B51|A Chain A, Structural Basis For Utp Specificity Of Rna Editing
Tutases From Trypanosoma Brucei
pdb|2B56|A Chain A, Structural Basis For Utp Specificity Of Rna Editing
Tutases From Trypanosoma Brucei
Length = 468
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 33/129 (25%), Positives = 53/129 (41%), Gaps = 17/129 (13%)
Query: 499 VVNTKLLRDYAQI-DVRLQQLAFIVKHWAKSRGVNVTYQGTLSSYAYVLMCIHFLQQRRP 557
V N+ L+R Y V + A VK W K+ V L+SYA +M I++L R
Sbjct: 256 VKNSYLIRHYLHNGPVAARHTAMAVKAWGKATNVGAGSGAMLTSYAVTVMFIYYLLVTRQ 315
Query: 558 AILPCLQGMEKTYSVTVDDIECAYFDQVDKLHGFGSR---NKESIGRLVWAFFNYWAYGH 614
+ VD + + + F + +GRL+ FF ++A+
Sbjct: 316 VLW-------------VDPWSLPHPAHLPRYPDFSPLYDCDPTELGRLLHGFFIFYAHHF 362
Query: 615 DYASNVISV 623
DY V+S+
Sbjct: 363 DYEREVVSL 371
>pdb|2B4V|A Chain A, Structural Basis For Utp Specificity Of Rna Editing
Tutases From Trypanosoma Brucei
Length = 468
Score = 35.8 bits (81), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 35/138 (25%), Positives = 52/138 (37%), Gaps = 35/138 (25%)
Query: 499 VVNTKLLRDYAQI-DVRLQQLAFIVKHWAKSRGVNVTYQGTLSSYAYVLMCIHFLQQRR- 556
V N+ L+R Y V + A VK W K+ V L+SYA + I++L R
Sbjct: 256 VKNSYLIRHYLHNGPVAARHTAXAVKAWGKATNVGAGSGAXLTSYAVTVXFIYYLLVTRQ 315
Query: 557 -----------PAILPCLQGMEKTYSVTVDDIECAYFDQVDKLHGFGSRNKESIGRLVWA 605
PA LP Y +C + +GRL+
Sbjct: 316 VLWVDPWSLPHPAHLPRYPDFSPLY-------DC---------------DPTELGRLLHG 353
Query: 606 FFNYWAYGHDYASNVISV 623
FF ++A+ DY V+S+
Sbjct: 354 FFIFYAHHFDYEREVVSL 371
>pdb|3IZQ|1 Chain 1, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
Translating Ribosome
Length = 611
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/32 (53%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 301 YSQGGDDMDDF-GEDLVDSLLPDDESELKNDT 331
YS G DDM DF E D L DDE EL N+
Sbjct: 6 YSDGADDMPDFHDEGEFDDYLNDDEYELMNEV 37
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 0.136 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,996,189
Number of Sequences: 62578
Number of extensions: 630999
Number of successful extensions: 1149
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1119
Number of HSP's gapped (non-prelim): 16
length of query: 630
length of database: 14,973,337
effective HSP length: 105
effective length of query: 525
effective length of database: 8,402,647
effective search space: 4411389675
effective search space used: 4411389675
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: 54 (25.4 bits)