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= psy8191
(257 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
Synthase Rlud From Escherichia Coli
pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
Length = 325
Score = 187 bits (476), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 102/238 (42%), Positives = 146/238 (61%), Gaps = 17/238 (7%)
Query: 23 EKKVIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHR 82
E + I LDI+YED +III+NK LVVHP GN GT+ + LL YP + +VPRAGIVHR
Sbjct: 77 EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR 136
Query: 83 LDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRI 142
LDK+++GLMVVAK++ + LV L+ + R+Y A+ G G ++ I R+P R
Sbjct: 137 LDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRT 196
Query: 143 KMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDN 202
M V + KPA+T+Y + ++ + +R L+TGRTHQIRVHM + H +VGD
Sbjct: 197 HMAV--HPMGKPAVTHYRIMEHFRVHTR----LRLRLETGRTHQIRVHMAHITHPLVGDP 250
Query: 203 LYG------KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
+YG K S++ I F+RQALHA L L HP + ++++W +P D+ +LI
Sbjct: 251 VYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELI 308
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 179 bits (455), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 98/238 (41%), Positives = 140/238 (58%), Gaps = 17/238 (7%)
Query: 23 EKKVIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHR 82
E + I LDI+YED +II++NK LVVHP GN GT+ + LL YP + +VPRAGIVHR
Sbjct: 4 EPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR 63
Query: 83 LDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRI 142
LDK+++GL VVAK++ + LV L+ + R+Y A+ G G ++ I R+P R
Sbjct: 64 LDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGHXTAGGTVDEPISRHPTKRT 123
Query: 143 KMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDN 202
V + KPA+T+Y ++ + +R L+TGRTHQIRVH + H +VGD
Sbjct: 124 HXAV--HPXGKPAVTHYRIXEHFRVHTR----LRLRLETGRTHQIRVHXAHITHPLVGDP 177
Query: 203 LYG------KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
+YG K S++ I F+RQALHA L L HP + ++ +W +P D +LI
Sbjct: 178 VYGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVELI 235
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 179 bits (453), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 99/238 (41%), Positives = 140/238 (58%), Gaps = 17/238 (7%)
Query: 23 EKKVIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHR 82
E + I LDI+YED +III+NK LVVHP GN GT+ + LL YP + +VPRAGIVHR
Sbjct: 101 EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR 160
Query: 83 LDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRI 142
LDK+++GL VVAK++ + LV L+ + R+Y A+ G G ++ I R+P R
Sbjct: 161 LDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGHXTAGGTVDEPISRHPTKRT 220
Query: 143 KMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDN 202
V + KPA+T+Y ++ + +R L+TGRTHQIRVH + H +VGD
Sbjct: 221 HXAV--HPMGKPAVTHYRIXEHFRVHTR----LRLRLETGRTHQIRVHXAHITHPLVGDP 274
Query: 203 LYG------KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
+YG K S++ I F+RQALHA L L HP + ++ +W +P D +LI
Sbjct: 275 VYGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVELI 332
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
pdb|1XPI|B Chain B, Crystal Structure Of The Catalytic Domain Of E. Coli
Pseudouridine Synthase Rluc
Length = 231
Score = 107 bits (267), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 79/227 (34%), Positives = 119/227 (52%), Gaps = 29/227 (12%)
Query: 31 IIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYP---FLINVPRAGIVHRLDKNS 87
I+YED+ I++LNK +G VH G LS + + L + P FL +VHRLD+++
Sbjct: 7 ILYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPEARFL------ELVHRLDRDT 59
Query: 88 SGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLN-GMINAAIMRNPHNRIKMTV 146
SG+++VAK + L QL+ +Q+ YLA+V G + + + A +++N + V
Sbjct: 60 SGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIV 119
Query: 147 SKNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNL 203
+ KP+ T + ER A +L+RC+ TGRTHQIRVH Q+ GH I D+
Sbjct: 120 RVSQEGKPSETRFKVEERYAFA-------TLVRCSPVTGRTHQIRVHTQYAGHPIAFDDR 172
Query: 204 YG-KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDD 244
YG +++ + L NR LHA L HP + RI P D
Sbjct: 173 YGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVM--RIEAPMD 217
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
pdb|1V9K|B Chain B, The Crystal Structure Of The Catalytic Domain Of
Pseudouridine Synthase Rluc From Escherichia Coli
Length = 228
Score = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 79/227 (34%), Positives = 116/227 (51%), Gaps = 29/227 (12%)
Query: 31 IIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYP---FLINVPRAGIVHRLDKNS 87
I YED+ I++LNK +G VH G LS + + L + P FL +VHRLD+++
Sbjct: 4 IXYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPEARFLE------LVHRLDRDT 56
Query: 88 SGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLN-GMINAAIMRNPHNRIKMTV 146
SG+++VAK + L QL+ Q+ YLA+V G + + + A +++N + V
Sbjct: 57 SGVLLVAKKRSALRSLHEQLREKGXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIV 116
Query: 147 SKNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNL 203
+ KP+ T + ER A +L+RC+ TGRTHQIRVH Q+ GH I D+
Sbjct: 117 RVSQEGKPSETRFKVEERYA-------FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDR 169
Query: 204 YG-KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDD 244
YG +++ + L NR LHA L HP RI P D
Sbjct: 170 YGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVX--RIEAPXD 214
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|B Chain B, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|C Chain C, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
pdb|2I82|D Chain D, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect
Sequence Readout Through Protein-induced Rna Structure
Length = 217
Score = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 105/201 (52%), Gaps = 13/201 (6%)
Query: 31 IIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLI-NVPRAGIVHRLDKNSSG 89
I+Y+D+ I ++NK +GL+ ++ G L ++ + + + P+A VHRLD +SG
Sbjct: 14 ILYQDDHIXVVNKPSGLL------SVPGRLEEHKDSVXTRIQRDYPQAESVHRLDXATSG 67
Query: 90 LMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPK-LNGMINAAIMRNPHNRIKMTVSK 148
++VVA + + L Q + +++Y+A VWG P G+++ ++ + NR K V
Sbjct: 68 VIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY 127
Query: 149 NFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYGKKY 208
KPA T YE + N + L TGR+HQ+RVH LGH I+GD Y
Sbjct: 128 E-TGKPAQTEYEVVEYAADNTARVVL---KPITGRSHQLRVHXLALGHPILGDRFYASPE 183
Query: 209 SKSLIFNRQALHAYKLGLIHP 229
+++ R LHA L + HP
Sbjct: 184 ARAXA-PRLLLHAEXLTITHP 203
>pdb|1KJZ|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant
pdb|1KK1|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdpnp-Mg2+
pdb|1KK2|A Chain A, Structure Of The Large Gamma Subunit Of Initiation Factor
Eif2 From Pyrococcus Abyssi-G235d Mutant Complexed With
Gdp-Mg2+
Length = 410
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 136 RNPHNRIKMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLG 195
R+P+ KM V ++F+ T E+L G+++ S+++ LK G +IR + +
Sbjct: 203 RDPNKPPKMLVLRSFDVNKPGTPPEKLVGGVLDG---SIVQGKLKVGDEIEIRPGVPYEE 259
Query: 196 HG 197
HG
Sbjct: 260 HG 261
>pdb|3G1N|A Chain A, Catalytic Domain Of The Human E3 Ubiquitin-Protein Ligase
Huwe1
pdb|3G1N|B Chain B, Catalytic Domain Of The Human E3 Ubiquitin-Protein Ligase
Huwe1
Length = 388
Score = 31.2 bits (69), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 70 FLINVPRAGI--VHRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLA 118
F V G+ V L N + ++V ++ K Y+HLV Q++M RK LA
Sbjct: 188 FSTEVQEFGVCEVRDLKPNGANILVTEENKKEYVHLVCQMRMTGAIRKQLA 238
>pdb|3H1D|A Chain A, Structure Of The Huwe1 Hect Domain
Length = 405
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 70 FLINVPRAGI--VHRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLA 118
F V G+ V L N + ++V ++ K Y+HLV Q++M RK LA
Sbjct: 205 FSTEVQEFGVAEVRDLKPNGANILVTEENKKEYVHLVCQMRMTGAIRKQLA 255
>pdb|3PE7|A Chain A, Oligogalacturonate Lyase In Complex With Manganese
Length = 388
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 156 LTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGI 198
LT +++ K L+R +LKTG + I QWLGH I
Sbjct: 152 LTDWKKFHEFYFTKPCCRLMRVDLKTGESTVILQENQWLGHPI 194
>pdb|1KK3|A Chain A, Structure Of The Wild-Type Large Gamma Subunit Of
Initiation Factor Eif2 From Pyrococcus Abyssi Complexed
With Gdp-Mg2+
Length = 410
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 136 RNPHNRIKMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLG 195
R+P+ KM V ++F+ T E+L G++ S+++ LK G +IR + +
Sbjct: 203 RDPNKPPKMLVLRSFDVNKPGTPPEKLVGGVLGG---SIVQGKLKVGDEIEIRPGVPYEE 259
Query: 196 HG 197
HG
Sbjct: 260 HG 261
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
0.324 0.141 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,623,223
Number of Sequences: 62578
Number of extensions: 306533
Number of successful extensions: 792
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 771
Number of HSP's gapped (non-prelim): 11
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)