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= 006140
(659 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 62/146 (42%), Gaps = 16/146 (10%)
Query: 88 EVFPFGSVPLKTYLPDGDIDLTVLGHQNVEEDLARFVCKILENEDQDSVFEIKDVQYVPA 147
E+ FGS+ L + D+DL VL V+ D + E FE K +Q A
Sbjct: 56 ELVAFGSLESGLALKNSDMDLCVLMDSRVQSDT---IALQFYEELIAEGFEGKFLQ--RA 110
Query: 148 QVKIVKCSVQ-------NIPVDISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAW 200
++ I+K + + DI FN + L +L D K V+L+K W
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHW 167
Query: 201 CYYESRILGAHYGLISTYALEMMVLH 226
+I ++G +S+Y +MVL+
Sbjct: 168 A-KRKQINSPYFGTLSSYGYVLMVLY 192
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 287 TALENTGHEFAIKH----LNIVDPLKDNNNLGRSVSKGNFHRIR 326
+A E+TG I L I DP + +NN+GR+VS +RIR
Sbjct: 280 SATEHTGSADQIIKDRYILAIEDPFEISNNVGRTVSSSGLYRIR 323
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 62/146 (42%), Gaps = 16/146 (10%)
Query: 88 EVFPFGSVPLKTYLPDGDIDLTVLGHQNVEEDLARFVCKILENEDQDSVFEIKDVQYVPA 147
E+ FGS+ L + D+DL VL V+ D + E FE K +Q A
Sbjct: 56 ELVAFGSLESGLALKNSDMDLCVLMDSRVQSDT---IALQFYEELIAEGFEGKFLQ--RA 110
Query: 148 QVKIVKCSVQ-------NIPVDISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAW 200
++ I+K + + DI FN + L +L D K V+L+K W
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHW 167
Query: 201 CYYESRILGAHYGLISTYALEMMVLH 226
+I ++G +S+Y +MVL+
Sbjct: 168 A-KRKQINSPYFGTLSSYGYVLMVLY 192
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 62/146 (42%), Gaps = 16/146 (10%)
Query: 88 EVFPFGSVPLKTYLPDGDIDLTVLGHQNVEEDLARFVCKILENEDQDSVFEIKDVQYVPA 147
E+ FGS+ L + D+DL VL V+ D + E FE K +Q A
Sbjct: 84 ELVAFGSLESGLALKNSDMDLCVLMDSRVQSDT---IALQFYEELIAEGFEGKFLQR--A 138
Query: 148 QVKIVKCSVQ-------NIPVDISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAW 200
++ I+K + + DI FN + L +L D K V+L+K W
Sbjct: 139 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHW 195
Query: 201 CYYESRILGAHYGLISTYALEMMVLH 226
+I ++G +S+Y +MVL+
Sbjct: 196 A-KRKQINSPYFGTLSSYGYVLMVLY 220
>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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 39/146 (26%), Positives = 62/146 (42%), Gaps = 16/146 (10%)
Query: 88 EVFPFGSVPLKTYLPDGDIDLTVLGHQNVEEDLARFVCKILENEDQDSVFEIKDVQYVPA 147
E+ FGS+ L + D+DL VL V+ D + E FE K +Q A
Sbjct: 47 ELVAFGSLESGLALKNSDMDLCVLMDSRVQSDT---IALQFYEELIAEGFEGKFLQ--RA 101
Query: 148 QVKIVKCSVQ-------NIPVDISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAW 200
++ I+K + + DI FN + L +L D K V+L+K W
Sbjct: 102 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKL---DARLKPMVLLVKHW 158
Query: 201 CYYESRILGAHYGLISTYALEMMVLH 226
+I ++G +S+Y +MVL+
Sbjct: 159 A-KRKQINSPYFGTLSSYGYVLMVLY 183
>pdb|3IWJ|A Chain A, Crystal Structure Of Aminoaldehyde Dehydrogenase 2 From
Pisum Sativum (Psamadh2)
pdb|3IWJ|B Chain B, Crystal Structure Of Aminoaldehyde Dehydrogenase 2 From
Pisum Sativum (Psamadh2)
Length = 503
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 82/198 (41%), Gaps = 37/198 (18%)
Query: 205 SRILGAHYGLISTYALEM-----MVLHRFLDYYNTFDWDNY-CISINGPVAISSLPEIVA 258
S+I+ A L+ +LE+ +V+ +D +W + C NG + ++ I+
Sbjct: 244 SKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILH 303
Query: 259 ETVENDGDELLLSPEFLKKCREIYSVPITALENTGHEFAIKHLNIVDPLKDNNNLGRSVS 318
E++ + EFL + + IK++ I DPL++ LG VS
Sbjct: 304 ESI---------ATEFLNRIVKW----------------IKNIKISDPLEEGCRLGPVVS 338
Query: 319 KGNFHRIRCALSYGAQRLGEILT---LPGHC-LGMGLEKFFINTLERNGKGLRPDVQVPI 374
+G + +I +S ILT P H G +E I + N + R +V P+
Sbjct: 339 EGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPV 398
Query: 375 HAFG--SGKSEAADLSGD 390
S + EA DL+ D
Sbjct: 399 LCVKTFSTEEEAIDLAND 416
>pdb|1VEF|A Chain A, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
pdb|1VEF|B Chain B, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
pdb|1WKG|A Chain A, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
pdb|1WKG|B Chain B, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
pdb|1WKH|A Chain A, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
pdb|1WKH|B Chain B, Acetylornithine Aminotransferase From Thermus Thermophilus
Hb8
Length = 395
Score = 36.2 bits (82), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 34/117 (29%), Positives = 47/117 (40%), Gaps = 11/117 (9%)
Query: 256 IVAETVENDGDELLLSPEFLKKCREIYSVP---------ITALENTGHEFAIKHLNIV-D 305
++ E V+ +G +PEFL+ REI T + TG FA +H IV D
Sbjct: 189 VILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPD 248
Query: 306 PLKDNNNLGRSVSKGNFHRIRCALSYGAQRLGEILTLPGHCLGMGLEKFFINTLERN 362
L LG V G +R ++ + G T G+ L M I LER
Sbjct: 249 ILTLAKALGGGVPLG-VAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERT 304
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 32.7 bits (73), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 43/184 (23%), Positives = 78/184 (42%), Gaps = 13/184 (7%)
Query: 46 WLLAEERIQEILCTIQPAIVSEKKRKEVINYIQRLINGYY-GIEVFPFGSVPLKTYLPDG 104
WL E I++ + I P+ + R + I+ I+ + + ++ FGS YLP
Sbjct: 20 WLTFE--IKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGS 77
Query: 105 DIDLTV---LGHQNVEEDLARFVCKILENEDQDSVFEIKDVQYVPAQVKIVKCSVQNIPV 161
DID V LG + +L L+ ++ + E+ VP +K V+ I +
Sbjct: 78 DIDCVVTSELGGKESRNNLYSLASH-LKKKNLATEVEVVAKARVPI-IKFVEPH-SGIHI 134
Query: 162 DISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAWCYYESRILGAHYGLISTYALE 221
+SF + G+ A K+ R D R ++LI + R+ H G + +++
Sbjct: 135 AVSFERTNGIEA----AKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGGFSII 190
Query: 222 MMVL 225
+V
Sbjct: 191 CLVF 194
>pdb|4I8P|A Chain A, Crystal Structure Of Aminoaldehyde Dehydrogenase 1a From
Zea Mays (zmamadh1a)
pdb|4I8P|B Chain B, Crystal Structure Of Aminoaldehyde Dehydrogenase 1a From
Zea Mays (zmamadh1a)
Length = 520
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 299 KHLNIVDPLKDNNNLGRSVSKGNFHRIRCALSYGAQRLGEILT---LPGHCLGMGLEK-F 354
K++ + DPL++ LG VS+G + +I+ +S + ILT P H LEK F
Sbjct: 336 KNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGGVRPAH-----LEKGF 390
Query: 355 FI 356
FI
Sbjct: 391 FI 392
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 86 GIEVFPFGSVPLKTYLPDGDIDLTVLGHQNVEED--LARFVCKILENEDQDSVFEIKDVQ 143
G ++F FGS L + DID + ++V+ F K+ E E+KD++
Sbjct: 94 GGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQE------EVKDLR 147
Query: 144 YV-PAQVKIVKCSVQNIPVDISFNQMA 169
V A V ++K I +DI F ++A
Sbjct: 148 AVEEAFVPVIKLXFDGIEIDILFARLA 174
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 86 GIEVFPFGSVPLKTYLPDGDIDLTVLGHQNVEED--LARFVCKILENEDQDSVFEIKDVQ 143
G ++F FGS L + DID + ++V+ F K+ E E+KD++
Sbjct: 94 GGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQE------EVKDLR 147
Query: 144 YV-PAQVKIVKCSVQNIPVDISFNQMA 169
V A V ++K I +DI F ++A
Sbjct: 148 AVEEAFVPVIKLCFDGIEIDILFARLA 174
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 86 GIEVFPFGSVPLKTYLPDGDIDLTVLGHQNVEED--LARFVCKILENEDQDSVFEIKDVQ 143
G ++F FGS L + DID + ++V+ F K+ E E+KD++
Sbjct: 94 GGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQE------EVKDLR 147
Query: 144 YV-PAQVKIVKCSVQNIPVDISFNQMA 169
V A V ++K I +DI F ++A
Sbjct: 148 AVEEAFVPVIKLCFDGIEIDILFARLA 174
>pdb|1NOZ|A Chain A, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOZ|B Chain B, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOY|A Chain A, Dna Polymerase (e.c.2.7.7.7)/dna Complex
pdb|1NOY|B Chain B, Dna Polymerase (e.c.2.7.7.7)/dna Complex
Length = 388
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 43/102 (42%), Gaps = 23/102 (22%)
Query: 204 ESRILGAHYGLISTYALEMMVLHRFLDYYNTFDWDNYCISINGPVAISSLPEIVAETVEN 263
+S++L YG Y+++ + + +LD Y F A ++LP E+V
Sbjct: 246 KSKLLQNMYGSKEIYSIDGVSILDYLDLYKKF-------------AFTNLPSFSLESV-- 290
Query: 264 DGDELLLSPEFLKKCREIYSVPITALENTGHEFAIKHLNIVD 305
+ KK + Y PI L T H+ I + NI+D
Sbjct: 291 -------AQHETKKGKLPYDGPINKLRETNHQRYISY-NIID 324
>pdb|1MVH|A Chain A, Structure Of The Set Domain Histone Lysine
Methyltransferase Clr4
pdb|1MVX|A Chain A, Structure Of The Set Domain Histone Lysine
Methyltransferase Clr4
Length = 299
Score = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 527 LPSRDNLESGCSLNVENGCSLNMENSCSLILSLEE 561
+P N +SGC+ + GC LN + C + L+E
Sbjct: 59 IPPDPNFQSGCNCSSLGGCDLNNPSRCECLDDLDE 93
>pdb|1W9Z|A Chain A, Structure Of Bannavirus Vp9
pdb|1W9Z|B Chain B, Structure Of Bannavirus Vp9
pdb|1W9Z|C Chain C, Structure Of Bannavirus Vp9
Length = 283
Score = 28.9 bits (63), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 145 VPAQVKIVKCSVQNIPVDISFNQMAGLSALCFLEKVDRLIGKDHLFKRSVILIKAWCY 202
+P+ VK+ K V+ I V + +M A C L ++ LI ++H F VI AW +
Sbjct: 28 LPSNVKLSKGEVEKIAV--TKKEMFDELAQCNLPTIE-LITREHTFNGDVIRFAAWLF 82
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
0.319 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,176,383
Number of Sequences: 62578
Number of extensions: 810216
Number of successful extensions: 1549
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1540
Number of HSP's gapped (non-prelim): 32
length of query: 659
length of database: 14,973,337
effective HSP length: 105
effective length of query: 554
effective length of database: 8,402,647
effective search space: 4655066438
effective search space used: 4655066438
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)