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= 000387
(1588 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 = 82.4 bits (202), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 87/343 (25%), Positives = 132/343 (38%), Gaps = 88/343 (25%)
Query: 1236 NWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEG 1295
N + + +++ LWP + ++FGS +T L LP SD+D VV E G E
Sbjct: 43 NQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVVT----------SELGGKES 92
Query: 1296 RNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPK 1355
RN + + LA + ++ V +PII V PH I A
Sbjct: 93 RNNLYSLASHLKKKNLATE-------VEVVAKARVPIIKFV--EPHSGIHIA-------- 135
Query: 1356 EDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTT 1415
S ++ I+AA +R
Sbjct: 136 ----------------------------VSFERTNGIEAAKLIR---------------- 151
Query: 1416 DLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQ-HEHHLGRP 1474
E + P L L++KQFL R L+ ++GGL + ++ L+ FL H +
Sbjct: 152 ----EWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGGFSIICLVFSFLHMHPRIITNE 207
Query: 1475 IN--QNYGRLLMDFLYFFGNVFDPRQMRI-SVQGSGVYIKRERGYSIDPIH------IDD 1525
I+ N G LL++F +G F + + S G VY + +I PI I D
Sbjct: 208 IDPKDNLGVLLIEFFELYGKNFGYDDVALGSSDGYPVYFPKSTWSAIQPIKNPFSLAIQD 267
Query: 1526 PRFPTNNVGRNCFRIHQCIKAFSDAYSILES---ELTSLTPAD 1565
P +NN+ R F I KAF+ A+ +L + EL S T D
Sbjct: 268 PGDESNNISRGSFNIRDIKKAFAGAFDLLTNRCFELHSATFKD 310
>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 = 43.5 bits (101), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 44/184 (23%), Positives = 78/184 (42%), Gaps = 41/184 (22%)
Query: 1393 KAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGG- 1451
K +V DI+ + G++ + L++ EQ P L++ +K++ L+ S GG
Sbjct: 148 KGGGAVDFDIT--AYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGS 205
Query: 1452 LSSYCLMLLITRFLQHEHHLG----------------------RPINQNY--GRLLMDFL 1487
++SY L++ +L +HL P ++ G ++DFL
Sbjct: 206 ITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFL 265
Query: 1488 YFFGNVFDPRQMRISVQGSGVYIKRERGYSI----------DPIH----IDDPRFPTNNV 1533
+FF + FD + IS+ G+ K E ++ + +H I+DP NV
Sbjct: 266 HFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNV 325
Query: 1534 GRNC 1537
GRN
Sbjct: 326 GRNV 329
>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 = 43.1 bits (100), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 53/236 (22%), Positives = 87/236 (36%), Gaps = 66/236 (27%)
Query: 1366 DNHVHSDMVALD----------------DSASPKCSHTSSDNIKAATSVRLDISFKSPSH 1409
D+ V SD +AL + P TS S + DI F +
Sbjct: 81 DSRVQSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCDIGFNN--R 138
Query: 1410 TGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQH-- 1467
+ T L+ T+ P+ L++K + + ++ Y G LSSY +L++ +L H
Sbjct: 139 LAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVI 198
Query: 1468 ---------------------------EHHLGRPINQNY---GRLLMDFLYFFGNVFDPR 1497
+ P +QNY G LL F F+ F+PR
Sbjct: 199 KPPVFPNLLLSPLKQEKIVDGFDVGFDDKLEDIPPSQNYSSLGSLLHGFFRFYAYKFEPR 258
Query: 1498 QMRISVQGSGVYI-KRERGYSIDPIH---------------IDDPRFPTNNVGRNC 1537
+ ++ + Y+ K+E+G++ H I+DP +NNVGR
Sbjct: 259 EKVVTFRRPDGYLTKQEKGWTSATEHTGSADQIIKDRYILAIEDPFEISNNVGRTV 314
>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 = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 46/204 (22%), Positives = 78/204 (38%), Gaps = 50/204 (24%)
Query: 1382 PKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLAD 1441
P TS S + DI F + + T L+ T+ P+ L++K +
Sbjct: 141 PIIKLTSDTKNGFGASFQCDIGFNN--RLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 198
Query: 1442 RSLDQSYSGGLSSYCLMLLITRFLQH-----------------------------EHHLG 1472
+ ++ Y G LSSY +L++ +L H +
Sbjct: 199 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 258
Query: 1473 RPINQNY---GRLLMDFLYFFGNVFDPRQMRISVQGSGVYI-KRERGYSIDPIH------ 1522
P +QNY G LL F F+ F+PR+ ++ + Y+ K+E+G++ H
Sbjct: 259 IPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQ 318
Query: 1523 ---------IDDPRFPTNNVGRNC 1537
I+DP ++NVGR
Sbjct: 319 IIKDRYILAIEDPFEISHNVGRTV 342
>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 = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 46/204 (22%), Positives = 78/204 (38%), Gaps = 50/204 (24%)
Query: 1382 PKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLAD 1441
P TS S + DI F + + T L+ T+ P+ L++K +
Sbjct: 113 PIIKLTSDTKNGFGASFQCDIGFNN--RLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 170
Query: 1442 RSLDQSYSGGLSSYCLMLLITRFLQH-----------------------------EHHLG 1472
+ ++ Y G LSSY +L++ +L H +
Sbjct: 171 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 230
Query: 1473 RPINQNY---GRLLMDFLYFFGNVFDPRQMRISVQGSGVYI-KRERGYSIDPIH------ 1522
P +QNY G LL F F+ F+PR+ ++ + Y+ K+E+G++ H
Sbjct: 231 IPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQ 290
Query: 1523 ---------IDDPRFPTNNVGRNC 1537
I+DP ++NVGR
Sbjct: 291 IIKDRYILAIEDPFEISHNVGRTV 314
>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 = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 46/204 (22%), Positives = 78/204 (38%), Gaps = 50/204 (24%)
Query: 1382 PKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLAD 1441
P TS S + DI F + + T L+ T+ P+ L++K +
Sbjct: 104 PIIKLTSDTKNGFGASFQCDIGFNN--RLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKR 161
Query: 1442 RSLDQSYSGGLSSYCLMLLITRFLQH-----------------------------EHHLG 1472
+ ++ Y G LSSY +L++ +L H +
Sbjct: 162 KQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFPNLLLSPLKQEKIVDGFDVGFDDKLED 221
Query: 1473 RPINQNY---GRLLMDFLYFFGNVFDPRQMRISVQGSGVYI-KRERGYSIDPIH------ 1522
P +QNY G LL F F+ F+PR+ ++ + Y+ K+E+G++ H
Sbjct: 222 IPPSQNYSSLGSLLHGFFRFYAYKFEPREKVVTFRRPDGYLTKQEKGWTSATEHTGSADQ 281
Query: 1523 ---------IDDPRFPTNNVGRNC 1537
I+DP ++NVGR
Sbjct: 282 IIKDRYILAIEDPFEISHNVGRTV 305
>pdb|4J40|A Chain A, Crystal Structure Of The Dual-domain Ggdef-eal Module Of
Fimx From Pseudomonas Aeruginosa
pdb|4J40|B Chain B, Crystal Structure Of The Dual-domain Ggdef-eal Module Of
Fimx From Pseudomonas Aeruginosa
Length = 437
Score = 35.8 bits (81), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 65/127 (51%), Gaps = 12/127 (9%)
Query: 87 IQMLGKLRANGH--GFFIILPDLPSRDPPYLP--GLCYKKSR----GLLSRVAESNESG- 137
I++L + RA GH F+ L +DP LP G+ K +R L+ +++E++ +
Sbjct: 261 IKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSY 320
Query: 138 -RWVFESTRLFSSREGEK-IEEWSCPVNCLDTFT-VSVEFVENVDRFIDIMDEISNGGFL 194
+ + T+ ++ + I ++ C +N + ++V+F++ F+ ++++ N L
Sbjct: 321 LKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEIL 380
Query: 195 RGEESEL 201
+G +EL
Sbjct: 381 KGLIAEL 387
>pdb|3HV8|A Chain A, Crystal Structure Of Fimx Eal Domain From Pseudomonas
Aeruginosa Bound To C-Di-Gmp
Length = 268
Score = 35.8 bits (81), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 65/127 (51%), Gaps = 12/127 (9%)
Query: 87 IQMLGKLRANGH--GFFIILPDLPSRDPPYLP--GLCYKKSR----GLLSRVAESNESG- 137
I++L + RA GH F+ L +DP LP G+ K +R L+ +++E++ +
Sbjct: 92 IKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSY 151
Query: 138 -RWVFESTRLFSSREGEK-IEEWSCPVNCLDTFT-VSVEFVENVDRFIDIMDEISNGGFL 194
+ + T+ ++ + I ++ C +N + ++V+F++ F+ ++++ N L
Sbjct: 152 LKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEIL 211
Query: 195 RGEESEL 201
+G +EL
Sbjct: 212 KGLIAEL 218
>pdb|4AFY|A Chain A, Crystal Structure Of The Fimx Eal Domain In Complex With
Reaction Product Pgpg
pdb|4AFY|B Chain B, Crystal Structure Of The Fimx Eal Domain In Complex With
Reaction Product Pgpg
pdb|4AG0|A Chain A, Crystal Structure Of Fimx Eal Domain
pdb|4AG0|B Chain B, Crystal Structure Of Fimx Eal Domain
Length = 274
Score = 35.4 bits (80), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 65/127 (51%), Gaps = 12/127 (9%)
Query: 87 IQMLGKLRANGH--GFFIILPDLPSRDPPYLP--GLCYKKSR----GLLSRVAESNESG- 137
I++L + RA GH F+ L +DP LP G+ K +R L+ +++E++ +
Sbjct: 98 IKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSY 157
Query: 138 -RWVFESTRLFSSREGEK-IEEWSCPVNCLDTFT-VSVEFVENVDRFIDIMDEISNGGFL 194
+ + T+ ++ + I ++ C +N + ++V+F++ F+ ++++ N L
Sbjct: 158 LKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEIL 217
Query: 195 RGEESEL 201
+G +EL
Sbjct: 218 KGLIAEL 224
>pdb|3HV9|A Chain A, Crystal Structure Of Fimx Eal Domain From Pseudomonas
Aeruginosa
Length = 265
Score = 32.0 bits (71), Expect = 2.5, Method: Composition-based stats.
Identities = 29/127 (22%), Positives = 65/127 (51%), Gaps = 12/127 (9%)
Query: 87 IQMLGKLRANGH--GFFIILPDLPSRDPPYLP--GLCYKKSR----GLLSRVAESNESG- 137
I++L + RA GH F+ L +DP LP G+ K +R L+ +++E++ +
Sbjct: 89 IKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSY 148
Query: 138 -RWVFESTRLFSSREGEK-IEEWSCPVNCLDTFT-VSVEFVENVDRFIDIMDEISNGGFL 194
+ + T+ ++ + I ++ C +N + ++V+F++ F+ ++++ N L
Sbjct: 149 LKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEIL 208
Query: 195 RGEESEL 201
+G +EL
Sbjct: 209 KGLIAEL 215
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 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,206,181
Number of Sequences: 62578
Number of extensions: 1700876
Number of successful extensions: 3525
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 3513
Number of HSP's gapped (non-prelim): 17
length of query: 1588
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1476
effective length of database: 7,964,601
effective search space: 11755751076
effective search space used: 11755751076
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: 58 (26.9 bits)