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= psy7666
(350 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NKS|A Chain A, Structure Of Human Protoporphyrinogen Ix Oxidase
Length = 477
Score = 191 bits (485), Expect = 6e-49, Method: Compositional matrix adjust.
Identities = 95/224 (42%), Positives = 137/224 (61%), Gaps = 7/224 (3%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPITS 156
+ L+ESS RLGGW+RSV+ P G IFE GPR IRP G LGA TL LV +LGL +V+P+
Sbjct: 30 VVLVESSERLGGWIRSVRGPNGAIFELGPRGIRPAGALGARTLLLVSELGLDSEVLPVRG 89
Query: 157 SHPTAQNRLIYVNKKLHKLPSNFFSLFKTHSPFSKPLIFSILHDLTTKTVPKSDESIYDF 216
HP AQNR +YV LH LP+ L + PFSKPL ++ L +LT + DE+++ F
Sbjct: 90 DHPAAQNRFLYVGGALHALPTGLRGLLRPSPPFSKPLFWAGLRELTKPRGKEPDETVHSF 149
Query: 217 VSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGAIKEM-MSK 275
RR G EVA A+ S+ G+ AG+++++S+ LF+ EQ H ++ G + +
Sbjct: 150 AQRRLGPEVASLAMDSLCRGVFAGNSRELSIRSCFPSLFQAEQTHRSILLGLLLGAGRTP 209
Query: 276 RPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNK 319
+PD S L R++ E+WS WS+ GGL+ + L HL+++
Sbjct: 210 QPD------SALIRQALAERWSQWSLRGGLEMLPQALETHLTSR 247
>pdb|3I6D|A Chain A, Crystal Structure Of Ppo From Bacillus Subtilis With Af
pdb|3I6D|B Chain B, Crystal Structure Of Ppo From Bacillus Subtilis With Af
Length = 470
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 64/228 (28%), Positives = 117/228 (51%), Gaps = 27/228 (11%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPITS 156
+TL+E+S R+GG +++V+ +G I E+GP + + + + +LV+DLGL ++
Sbjct: 37 LTLVEASPRVGGKIQTVKK-DGYIIERGPDSFLERKK---SAPQLVKDLGLEHLLV---- 88
Query: 157 SHPTAQNRLIYVNKKLHKLPSNFFSLFKTH-SPFSKPLIFSI-------LHDLTTKTVPK 208
++ T Q+ ++ VN+ LH +P T +PF +FS+ + + + K
Sbjct: 89 NNATGQSYVL-VNRTLHPMPKGAVMGIPTKIAPFVSTGLFSLSGKARAAMDFILPASKTK 147
Query: 209 SDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGA 268
D+S+ +F RR G EV + + ++ GI AGD K+S+ + ++ EQ H +I G
Sbjct: 148 DDQSLGEFFRRRVGDEVVENLIEPLLSGIYAGDIDKLSLMSTFPQFYQTEQKHRSLILG- 206
Query: 269 IKEMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHL 316
M RP SG ++ ++ + + S GLQT+V + + L
Sbjct: 207 ---MKKTRPQGSG-QQLTAKKQGQFQTLST-----GLQTLVEEIEKQL 245
>pdb|1SEZ|A Chain A, Crystal Structure Of Protoporphyrinogen Ix Oxidase
pdb|1SEZ|B Chain B, Crystal Structure Of Protoporphyrinogen Ix Oxidase
Length = 504
Score = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 68/245 (27%), Positives = 112/245 (45%), Gaps = 23/245 (9%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPITS 156
+T+ E+ + GG +RSV S +GLI+++G T + L++ LGL ++
Sbjct: 39 VTVFEAEGKAGGKLRSV-SQDGLIWDEGANTXTESE---GDVTFLIDSLGLREK-----Q 89
Query: 157 SHPTAQN-RLIYVNKKLHKLPSNFFSLFKTHSPFSKPLIFSILHDLTTKT-----VPKSD 210
P +QN R I N LPSN L K++ + + +L + K V S
Sbjct: 90 QFPLSQNKRYIARNGTPVLLPSNPIDLIKSNFLSTGSKLQXLLEPILWKNKKLSQVSDSH 149
Query: 211 ESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGAIK 270
ES+ F R FG EV DY + + G C GD +S + +L+ LE+ G VI GAI+
Sbjct: 150 ESVSGFFQRHFGKEVVDYLIDPFVAGTCGGDPDSLSXHHSFPELWNLEKRFGSVILGAIR 209
Query: 271 EMMSKRPDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLS------NKVEVKM 324
+S + + + R + +S GG QT+ + + + L N +++
Sbjct: 210 SKLSPKNEKKQGPPKTSANKKR--QRGSFSFLGGXQTLTDAICKDLREDELRLNSRVLEL 267
Query: 325 DTTCT 329
+CT
Sbjct: 268 SCSCT 272
>pdb|2IVD|A Chain A, Structure Of Protoporphyrinogen Oxidase From Myxococcus
Xanthus With Acifluorfen
pdb|2IVD|B Chain B, Structure Of Protoporphyrinogen Oxidase From Myxococcus
Xanthus With Acifluorfen
pdb|2IVE|A Chain A, Structure Of Protoporphyrinogen Oxidase From Myxococcus
Xanthus
pdb|2IVE|B Chain B, Structure Of Protoporphyrinogen Oxidase From Myxococcus
Xanthus
Length = 478
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 64/243 (26%), Positives = 105/243 (43%), Gaps = 41/243 (16%)
Query: 94 STPITLLESSSRLGGWVRSVQSPEGLIFEKGPRTI---RPKGRLGANTLKLVEDLGLADQ 150
T LLESS+RLGG V + G + E+GP + P R A L L + AD
Sbjct: 39 GTDAVLLESSARLGGAV-GTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAAD- 96
Query: 151 VIPITSSHPTAQNRLIYVNKKLHKLPSNFFSLFKTHS-PFSKPLIFSILHDLTTKTVPKS 209
P A+ R +Y +L +P++ + + P L + +L ++ P+
Sbjct: 97 --------PAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARL--RVAGELFSRRAPEG 146
Query: 210 -DESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVIKGA 268
DES+ F R G + ++ GI AGD +++SV L ++E+ H +I GA
Sbjct: 147 VDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGA 206
Query: 269 IKEMMSKR---------PDLSGYEESELYRRSRIEKWSVWSVEGGLQTIVNTLGEHLSNK 319
I+ ++R P LSG ++ + +GGLQ +++ L L +
Sbjct: 207 IRAQKAQRQAALPAGTAPKLSG---------------ALSTFDGGLQVLIDALAASLGDA 251
Query: 320 VEV 322
V
Sbjct: 252 AHV 254
>pdb|3LOV|A Chain A, Crystal Structure Of Putative Protoporphyrinogen Oxidase
(Yp_001813199.1) From Exiguobacterium Sp. 255-15 At 2.06
A Resolution
Length = 475
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/182 (21%), Positives = 80/182 (43%), Gaps = 20/182 (10%)
Query: 97 ITLLESSSRLGGWVRSVQSPEGLIFEKGPRTIRPKGRLGANTLKLVEDLGLADQVIPITS 156
ITLLE+ RLGG V + + +G E+GP + + + + L+E +GL ++++ +
Sbjct: 32 ITLLEAGERLGGKVATYRE-DGFTIERGPDSYVARKHILTD---LIEAIGLGEKLVRNNT 87
Query: 157 SHPTAQNRLIYVNKKLHKLPSNF-------FSLFKTHSPFS----KPLIFSILHDLTTKT 205
S I LH +P LF+ + + + + +LH +
Sbjct: 88 SQA-----FILDTGGLHPIPKGAVXGIPTDLDLFRQTTLLTEEEKQEVADLLLHPSDSLR 142
Query: 206 VPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKLFELEQLHGGVI 265
+P+ D + +++ R G + + + ++ GI AG+ + S + EQ G +
Sbjct: 143 IPEQDIPLGEYLRPRLGDALVEKLIEPLLSGIYAGNIDQXSTFATYPQFVANEQKAGSLF 202
Query: 266 KG 267
+G
Sbjct: 203 EG 204
>pdb|2FOR|A Chain A, Crystal Structure Of The Shigella Flexneri Farnesyl
Pyrophosphate Synthase Complex With An Isopentenyl
Pyrophosphate
pdb|2FOR|B Chain B, Crystal Structure Of The Shigella Flexneri Farnesyl
Pyrophosphate Synthase Complex With An Isopentenyl
Pyrophosphate
Length = 323
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 14/84 (16%)
Query: 191 KPLIFSILHDLTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFL 250
+ L FSIL D V D S +++ A +S I G+C G A +
Sbjct: 142 QTLAFSILSDANMPEVSDRDRI----------SMISELASASGIAGMCGGQALDLDAEGK 191
Query: 251 MAKLFELEQLH----GGVIKGAIK 270
L LE++H G +I+ A++
Sbjct: 192 HVPLDALERIHRHKTGALIRAAVR 215
>pdb|1RQJ|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Risedronate
pdb|1RQJ|B Chain B, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Risedronate
Length = 299
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 14/82 (17%)
Query: 193 LIFSILHDLTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMA 252
L FSIL D V D S +++ A +S I G+C G A +
Sbjct: 120 LAFSILSDADMPEVSDRDRI----------SMISELASASGIAGMCGGQALDLDAEGKHV 169
Query: 253 KLFELEQLH----GGVIKGAIK 270
L LE++H G +I+ A++
Sbjct: 170 PLDALERIHRHKTGALIRAAVR 191
>pdb|1RQI|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Dimethylallyl S-
Thiolodiphosphate
pdb|1RQI|B Chain B, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Dimethylallyl S-
Thiolodiphosphate
Length = 300
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 14/82 (17%)
Query: 193 LIFSILHDLTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMA 252
L FSIL D V D S +++ A +S I G+C G A +
Sbjct: 121 LAFSILSDADMPEVSDRDRI----------SMISELASASGIAGMCGGQALDLDAEGKHV 170
Query: 253 KLFELEQLH----GGVIKGAIK 270
L LE++H G +I+ A++
Sbjct: 171 PLDALERIHRHKTGALIRAAVR 192
>pdb|4FMU|A Chain A, Crystal Structure Of Methyltransferase Domain Of Human Set
Domain- Containing Protein 2 Compound: Pr-Snf
pdb|4H12|A Chain A, The Crystal Structure Of Methyltransferase Domain Of Human
Set Domain- Containing Protein 2 In Complex With
S-Adenosyl-L-Homocysteine
Length = 278
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 23/54 (42%)
Query: 201 LTTKTVPKSDESIYDFVSRRFGSEVADYAVSSMICGICAGDAKKISVNFLMAKL 254
TTK VP E +D+ +R+G E S C G ++S+ K+
Sbjct: 218 FTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKM 271
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 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,198,773
Number of Sequences: 62578
Number of extensions: 339267
Number of successful extensions: 768
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 758
Number of HSP's gapped (non-prelim): 10
length of query: 350
length of database: 14,973,337
effective HSP length: 100
effective length of query: 250
effective length of database: 8,715,537
effective search space: 2178884250
effective search space used: 2178884250
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: 52 (24.6 bits)