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= psy13081
(335 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 70/245 (28%), Positives = 104/245 (42%), Gaps = 46/245 (18%)
Query: 4 IALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAF 63
IAL I Y G Y+G+Q Q ++ L KAL + E + C GRTD+GV
Sbjct: 12 IALGIEYDGSKYYGWQRQNEV-RSVQEKLEKALSQVA----NEPITVFCAGRTDAGVHGT 66
Query: 64 CQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 123
QVV + + + + +N NLP DI V VP+ + ARF R
Sbjct: 67 GQVVHFETTAL---------RKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARR 117
Query: 124 YKYWF------PQA----------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFR 167
Y+Y P LD + MH+AAQ L+G +DF +FR
Sbjct: 118 YRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDF------------TSFR 165
Query: 168 RLVTHAGVTSAWQNV-QFNDSHHN-ICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEI 225
+ + + W+NV N + H +I++ F+ H +R I+ L VG N+
Sbjct: 166 AVQCQS--RTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESW 223
Query: 226 IQQLV 230
I +L+
Sbjct: 224 IAELL 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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 70/245 (28%), Positives = 104/245 (42%), Gaps = 46/245 (18%)
Query: 4 IALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAF 63
IAL I Y G Y+G+Q Q ++ L KAL + E + C GRTD+GV
Sbjct: 6 IALGIEYDGSKYYGWQRQNEV-RSVQEKLEKALSQVA----NEPITVFCAGRTDAGVHGT 60
Query: 64 CQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRN 123
QVV + + + + +N NLP DI V VP+ + ARF R
Sbjct: 61 GQVVHFETTAL---------RKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARR 111
Query: 124 YKYWF------PQA----------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFR 167
Y+Y P LD + MH+AAQ L+G +DF +FR
Sbjct: 112 YRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDF------------TSFR 159
Query: 168 RLVTHAGVTSAWQNV-QFNDSHHN-ICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEI 225
+ + + W+NV N + H +I++ F+ H +R I+ L VG N+
Sbjct: 160 AVQCQS--RTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESW 217
Query: 226 IQQLV 230
I +L+
Sbjct: 218 IAELL 222
>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 = 71.2 bits (173), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 64/248 (25%), Positives = 97/248 (39%), Gaps = 44/248 (17%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
MR + L Y G + G Q Q T+ L +AL + GRTD+GV
Sbjct: 1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGAL-----PKAVAAGRTDAGV 55
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
A + + S + P E+ + LN LP D+KVV V + AR D L
Sbjct: 56 HALAMPFHVDVESAI--PVEKVPEA-------LNRLLPEDLKVVGAREVAPDFHARKDAL 106
Query: 121 FRNYKY-----------------WFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
+R Y+Y W + LD++AM +A L+G H+F K G
Sbjct: 107 WRAYRYRILVRPHPSPLLRHRALWVRRP-LDLEAMEEALSLLLGRHNFLGFAKEETRPGE 165
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNI-CEFNIRSQGFLWHQIRCIMSVLFLVGQGNEK 222
R L+ +Q + + R + FL Q+R ++ L VG G
Sbjct: 166 ---RELLE--------ARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRP 214
Query: 223 PEIIQQLV 230
PE ++ ++
Sbjct: 215 PESLKAIL 222
>pdb|3GGR|B Chain B, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex
Length = 286
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 28/123 (22%), Positives = 59/123 (47%), Gaps = 12/123 (9%)
Query: 31 HLLKALQKTCLIE-DKEKSSFACCGR-TDSGVSAFCQVVTLKIRSKLTSPGEESDDNELP 88
+++ L KTC + +K +F C + + GVS +C++ ++ G +++NE+
Sbjct: 27 NMIAKLAKTCTLRISPDKLNFILCDKLANGGVSMWCELEQENFFNEFQMEGVSAENNEI- 85
Query: 89 YLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGT 148
YL++ + NL R +K +AR + K+ FP + ++ + ++ + T
Sbjct: 86 YLELTSENLSRALKTA--------QNARALKIKLTNKH-FPCLTVSVELLSMSSSSRIVT 136
Query: 149 HDF 151
HD
Sbjct: 137 HDI 139
>pdb|3G65|C Chain C, Crystal Structure Of The Human Rad9-Rad1-Hus1 Dna Damage
Checkpoint Complex
Length = 280
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 28/123 (22%), Positives = 59/123 (47%), Gaps = 12/123 (9%)
Query: 31 HLLKALQKTCLIE-DKEKSSFACCGR-TDSGVSAFCQVVTLKIRSKLTSPGEESDDNELP 88
+++ L KTC + +K +F C + + GVS +C++ ++ G +++NE+
Sbjct: 21 NMIAKLAKTCTLRISPDKLNFILCDKLANGGVSMWCELEQENFFNEFQMEGVSAENNEI- 79
Query: 89 YLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGT 148
YL++ + NL R +K +AR + K+ FP + ++ + ++ + T
Sbjct: 80 YLELTSENLSRALKTA--------QNARALKIKLTNKH-FPCLTVSVELLSMSSSSRIVT 130
Query: 149 HDF 151
HD
Sbjct: 131 HDI 133
>pdb|2BTQ|B Chain B, Structure Of Btubab Heterodimer From Prosthecobacter
Dejongeii
Length = 426
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 107 SPVPEKYSARFDCLFRNYKY--WFPQAGLDIDAMHKA 141
+ V E+ A+FD +F N+ Y W+ AG+ D M KA
Sbjct: 375 AAVFERLIAQFDIMFDNHAYTHWYENAGVSRDMMAKA 411
>pdb|3A1J|B Chain B, Crystal Structure Of The Human Rad9-Hus1-Rad1 Complex
Length = 281
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 33 LKALQKTCLIE-DKEKSSFACCGR-TDSGVSAFCQVVTLKIRSKLTSPGEESDDNELPYL 90
+ L KTC + +K +F C + + GVS +C++ ++ G +++NE+ YL
Sbjct: 24 IAKLAKTCTLRISPDKLNFILCDKLANGGVSXWCELEQENFFNEFQXEGVSAENNEI-YL 82
Query: 91 KMLNNNLPRDIK 102
++ + NL R +K
Sbjct: 83 ELTSENLSRALK 94
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
0.322 0.137 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,679,759
Number of Sequences: 62578
Number of extensions: 445838
Number of successful extensions: 859
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 848
Number of HSP's gapped (non-prelim): 8
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)