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= 018562
(354 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 70/263 (26%), Positives = 109/263 (41%), Gaps = 60/263 (22%)
Query: 86 VLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKXXXXXXXXXXXXD 145
+LYED+ ++ +NKP G ++ G A R E D
Sbjct: 7 ILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLE----------LVHRLD 56
Query: 146 RDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAW 205
RDTSGV+++ K L + + + K Y+AL G W
Sbjct: 57 RDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQ--------------------W 96
Query: 206 RVYAASDVGRVLPGGSVVRDMVTSFE-VLSVNGEGSFKEPSELQEHEENNIVVEKKAVLD 264
+ + S ++++++ S E ++ V+ EG +PSE VE++
Sbjct: 97 QSHVKS------VQAPLLKNILQSGERIVRVSQEG---KPSE------TRFKVEERYAF- 140
Query: 265 ADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN------GKRYDGHE 318
LVR P +GRTHQIR+H QY G I D +Y G E++ G +
Sbjct: 141 ------ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY-GDREFDRQLTEAGTGLNRLF 193
Query: 319 LHAESLSFDHPVTGCPVMVQAPL 341
LHA +L F HP TG + ++AP+
Sbjct: 194 LHAAALKFTHPGTGEVMRIEAPM 216
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 69/262 (26%), Positives = 105/262 (40%), Gaps = 60/262 (22%)
Query: 86 VLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKXXXXXXXXXXXXD 145
+ YED+ ++ +NKP G ++ G A R E D
Sbjct: 4 IXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLE----------LVHRLD 53
Query: 146 RDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAW 205
RDTSGV+++ K L + + K Y+AL G W
Sbjct: 54 RDTSGVLLVAKKRSALRSLHEQLREKGXQKDYLALV--------------------RGQW 93
Query: 206 RVYAASDVGRVLPGGSVVRDMVTSFE-VLSVNGEGSFKEPSELQEHEENNIVVEKKAVLD 264
+ + S ++++++ S E ++ V+ EG +PSE VE++
Sbjct: 94 QSHVKS------VQAPLLKNILQSGERIVRVSQEG---KPSE------TRFKVEERYAF- 137
Query: 265 ADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN------GKRYDGHE 318
LVR P +GRTHQIR+H QY G I D +Y G E++ G +
Sbjct: 138 ------ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY-GDREFDRQLTEAGTGLNRLF 190
Query: 319 LHAESLSFDHPVTGCPVMVQAP 340
LHA +L F HP TG ++AP
Sbjct: 191 LHAAALKFTHPGTGEVXRIEAP 212
>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 = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 54/279 (19%), Positives = 107/279 (38%), Gaps = 82/279 (29%)
Query: 85 DVLYEDEWLVAVNKPQGVYCE--------SVLASVPCLLAGDSAESKSGRLSEGTKXXXX 136
D++YEDE ++ +NKP+ + +VL ++ + ++G +
Sbjct: 84 DIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR------- 136
Query: 137 XXXXXXXXDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISG 196
D+DT+G+MV+ K+ ++LV++ ++++ Y A+
Sbjct: 137 -------LDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVA--------------- 174
Query: 197 HGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSE---LQEHEEN 253
+G + GG+V E + P++ + H
Sbjct: 175 ----------------IGHMTAGGTV--------------DEPISRHPTKRTHMAVHPMG 204
Query: 254 NIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEG-------- 305
V +++ + +R +GRTHQIR+H ++ + GD Y G
Sbjct: 205 KPAVTHYRIMEHFRVHTRLRLRL--ETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGA 262
Query: 306 --VYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLP 342
+ +++D LHA L HP++G + AP+P
Sbjct: 263 SEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP 301
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic
Module
Length = 252
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 55/287 (19%), Positives = 104/287 (36%), Gaps = 82/287 (28%)
Query: 85 DVLYEDEWLVAVNKPQGVYCE--------SVLASVPCLLAGDSAESKSGRLSEGTKXXXX 136
D++YEDE ++ +NKP+ + +VL ++ + ++G +
Sbjct: 11 DIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR------- 63
Query: 137 XXXXXXXXDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISG 196
D+DT+G+ V+ K+ ++LV++ +++
Sbjct: 64 -------LDKDTTGLXVVAKTVPAQTRLVESLQRREIT---------------------- 94
Query: 197 HGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQE---HEEN 253
R Y A +G GG+V E + P++ H
Sbjct: 95 ---------REYEAVAIGHXTAGGTV--------------DEPISRHPTKRTHXAVHPXG 131
Query: 254 NIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEG-------- 305
V + + + +R +GRTHQIR+H ++ + GD Y G
Sbjct: 132 KPAVTHYRIXEHFRVHTRLRLRL--ETGRTHQIRVHXAHITHPLVGDPVYGGRPRPPKGA 189
Query: 306 --VYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQ 350
+ +++D LHA L HP++G AP+P E ++
Sbjct: 190 SEAFISTLRKFDRQALHATXLRLYHPISGIEXEWHAPIPQDXVELIE 236
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 280 SGRTHQIRLHCQYLGISIRGDVKYEG----------VYEWNGKRYDGHELHAESLSFDHP 329
+GRTHQIR+H ++ + GD Y G + +++D LHA L HP
Sbjct: 253 TGRTHQIRVHXAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATXLRLYHP 312
Query: 330 VTGCPVMVQAPLPLWGTEALQ 350
++G AP+P E ++
Sbjct: 313 ISGIEXEWHAPIPQDXVELIE 333
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/107 (21%), Positives = 51/107 (47%), Gaps = 22/107 (20%)
Query: 85 DVLYEDEWLVAVNKPQGVYCE--------SVLASVPCLLAGDSAESKSGRLSEGTKXXXX 136
D++YEDE ++ +NKP+ + +VL ++ + ++G +
Sbjct: 108 DIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHR------- 160
Query: 137 XXXXXXXXDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIG 183
D+DT+G+ V+ K+ ++LV++ ++++ Y A+ IG
Sbjct: 161 -------LDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIG 200
>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 = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 267 AKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHE--LHAESL 324
A N V P +GR+HQ+R+H LG I GD Y R LHAE L
Sbjct: 143 AADNTARVVLKPITGRSHQLRVHXLALGHPILGD----RFYASPEARAXAPRLLLHAEXL 198
Query: 325 SFDHPVTGCPVMVQAP 340
+ HP G +AP
Sbjct: 199 TITHPAYGNSXTFKAP 214
Score = 35.4 bits (80), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 12/102 (11%)
Query: 86 VLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKXXXXXXXXXXXXD 145
+LY+D+ + VNKP G L SVP L E + + D
Sbjct: 14 ILYQDDHIXVVNKPSG------LLSVPGRL-----EEHKDSVXTRIQRDYPQAESVHRLD 62
Query: 146 RDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIG-PAP 186
TSGV+V+ + +L + F + + K Y+A G P+P
Sbjct: 63 XATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSP 104
>pdb|3P0W|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Ralstonia Solanacearum Complexed With Mg And D-Glucarate
pdb|3P0W|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Ralstonia Solanacearum Complexed With Mg And D-Glucarate
pdb|3P0W|C Chain C, Crystal Structure Of D-Glucarate Dehydratase From
Ralstonia Solanacearum Complexed With Mg And D-Glucarate
pdb|3P0W|D Chain D, Crystal Structure Of D-Glucarate Dehydratase From
Ralstonia Solanacearum Complexed With Mg And D-Glucarate
Length = 470
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 7/112 (6%)
Query: 211 SDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKN 270
S + R L GG T +V S + ++P E+ +N I + A+LD +
Sbjct: 85 SSIRRALAGGGNAAHQATVHQVTSASEAAVLRQPHEINLRMDNVITAVEAALLDLLGQFL 144
Query: 271 EILVRAFPRSGRTHQ---IRLHCQYLGISIRGDVKY----EGVYEWNGKRYD 315
E+ V +G+ + + Y+G + D+ Y G +W R++
Sbjct: 145 EVPVAELLGAGQQRDSAPMLAYLFYVGDRRKTDLPYLEGANGADDWLRLRHE 196
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
0.315 0.132 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,769,276
Number of Sequences: 62578
Number of extensions: 378143
Number of successful extensions: 887
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 859
Number of HSP's gapped (non-prelim): 17
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
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: 52 (24.6 bits)