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= 015260
(410 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
pdb|1VS3|B Chain B, Crystal Structure Of The Trna Pseudouridine Synthase Trua
From Thermus Thermophilus Hb8
Length = 249
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 65/248 (26%), Positives = 96/248 (38%), Gaps = 51/248 (20%)
Query: 100 YFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSSVGQVIA 159
Y G F G G TV+ E+ +AL L GRTD GV ++
Sbjct: 10 YDGTLFAGLQRQGRGLRTVQGELERALPGIGAL------PKAVAAGRTDAGVHALAMPFH 63
Query: 160 IYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPTDFSARF 219
+ + S I A LNR+LP+D++V+G DF AR
Sbjct: 64 VDVESAIPVEKVPEA--------------------LNRLLPEDLKVVGAREVAPDFHARK 103
Query: 220 SCISREYKY---------------FFW-RENLNLSAMESAGKKFVGEHDFRNFCKMDAAN 263
+ R Y+Y W R L+L AME A +G H+F F K +
Sbjct: 104 DALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEE--- 160
Query: 264 VHNYKRHVTSFEISPCYISFEGNQLCAIKI--RGSAFLWHQVRCMVAVLFMIGQGLESID 321
+R + + EG +++ RG +FL QVR MV L +G G +
Sbjct: 161 TRPGERELLEARLQVA----EGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPE 216
Query: 322 VIESLLDT 329
++++L T
Sbjct: 217 SLKAILKT 224
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NQP|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|B Chain B, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|C Chain C, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NR0|D Chain D, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
pdb|2NRE|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In
Complex With Leucyl Trna
Length = 270
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 60/250 (24%), Positives = 102/250 (40%), Gaps = 49/250 (19%)
Query: 94 VALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSS 153
+AL + Y G ++YG+ + +V+ ++ KAL + VA++ + + GRTD GV
Sbjct: 12 IALGIEYDGSKYYGWQRQNEVR-SVQEKLEKALSQ----VANEPITVFC-AGRTDAGVHG 65
Query: 154 VGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPT 213
GQV+ + + + + +N LP DI V P
Sbjct: 66 TGQVVHF--------------------ETTALRKDAAWTLGVNANLPGDIAVRWVKTVPD 105
Query: 214 DFSARFSCISREYKYFFWR----------------ENLNLSAMESAGKKFVGEHDFRNFC 257
DF ARFS +R Y+Y + E L+ M A + +GE+DF +F
Sbjct: 106 DFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFR 165
Query: 258 KMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGL 317
+ + + R+V ++ + I+ +AF+ H VR +V L +G
Sbjct: 166 AVQCQSRTPW-RNVMHINVT------RHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHN 218
Query: 318 ESIDVIESLL 327
+ I LL
Sbjct: 219 QPESWIAELL 228
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
pdb|1DJ0|B Chain B, The Crystal Structure Of E. Coli Pseudouridine Synthase I
At 1.5 Angstrom Resolution
Length = 264
Score = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 60/250 (24%), Positives = 102/250 (40%), Gaps = 49/250 (19%)
Query: 94 VALKVMYFGQRFYGFASDGNMEPTVESEIFKALEKTRLLVADKKESHYSRCGRTDKGVSS 153
+AL + Y G ++YG+ + +V+ ++ KAL + VA++ + + GRTD GV
Sbjct: 6 IALGIEYDGSKYYGWQRQNEVR-SVQEKLEKALSQ----VANEPITVFC-AGRTDAGVHG 59
Query: 154 VGQVIAIYLRSNIKECNTNNASMGETVQEEQIEDEIDYVRVLNRVLPKDIRVIGWSPAPT 213
GQV+ + + + + +N LP DI V P
Sbjct: 60 TGQVVHF--------------------ETTALRKDAAWTLGVNANLPGDIAVRWVKTVPD 99
Query: 214 DFSARFSCISREYKYFFWR----------------ENLNLSAMESAGKKFVGEHDFRNFC 257
DF ARFS +R Y+Y + E L+ M A + +GE+DF +F
Sbjct: 100 DFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFR 159
Query: 258 KMDAANVHNYKRHVTSFEISPCYISFEGNQLCAIKIRGSAFLWHQVRCMVAVLFMIGQGL 317
+ + + R+V ++ + I+ +AF+ H VR +V L +G
Sbjct: 160 AVQCQSRTPW-RNVMHINVT------RHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHN 212
Query: 318 ESIDVIESLL 327
+ I LL
Sbjct: 213 QPESWIAELL 222
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
0.321 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,237,636
Number of Sequences: 62578
Number of extensions: 438143
Number of successful extensions: 785
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 774
Number of HSP's gapped (non-prelim): 3
length of query: 410
length of database: 14,973,337
effective HSP length: 101
effective length of query: 309
effective length of database: 8,652,959
effective search space: 2673764331
effective search space used: 2673764331
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)