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= 016811
(382 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 = 123 bits (308), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 99/315 (31%), Positives = 141/315 (44%), Gaps = 62/315 (19%)
Query: 51 MSTNKRIQRYLIA--VEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTD 108
MS ++ Y IA +EY G+++ G Q+Q R+V LE+A + +P+++ + RTD
Sbjct: 1 MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTD 60
Query: 109 AGVHAASNVCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDF 168
AGVH V H + + K + VN L GDI V V+ VP DF
Sbjct: 61 AGVHGTGQVVHFETTALRK-----------DAAWTLGVNANL--PGDIAVRWVKTVPDDF 107
Query: 169 HARFRAQERTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRA 228
HARF A R Y Y I + +V K H E LD M A + L+G +DF+SFRA
Sbjct: 108 HARFSATARRYRYIIYNHRLRPAVLSKGVT-HFYEPLDAERMHRAAQCLLGENDFTSFRA 166
Query: 229 SGCQANSPIRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKK 288
CQ+ +P R + ++V+ +
Sbjct: 167 VQCQSRTPWRNVMHINVT-----------------------------------------R 185
Query: 289 HRSYEVI-ARARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGL 347
H Y V+ +A +F++H VR IVG L VG S + +L AK T A+ A A GL
Sbjct: 186 HGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGL 245
Query: 348 SLGFV----KYDLPE 358
L V +YDLP+
Sbjct: 246 YLVAVDYPDRYDLPK 260
>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 = 122 bits (307), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 94/307 (30%), Positives = 137/307 (44%), Gaps = 60/307 (19%)
Query: 57 IQRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASN 116
+ + + +EY G+++ G Q+Q R+V LE+A + +P+++ + RTDAGVH
Sbjct: 3 VYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQ 62
Query: 117 VCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQE 176
V H + + K + VN L GDI V V+ VP DFHARF A
Sbjct: 63 VVHFETTALRK-----------DAAWTLGVNANL--PGDIAVRWVKTVPDDFHARFSATA 109
Query: 177 RTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSP 236
R Y Y I + +V K H E LD M A + L+G +DF+SFRA CQ+ +P
Sbjct: 110 RRYRYIIYNHRLRPAVLSKGVT-HFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTP 168
Query: 237 IRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVI- 295
R + ++V+ +H Y V+
Sbjct: 169 WRNVMHINVT-----------------------------------------RHGPYVVVD 187
Query: 296 ARARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFV--- 352
+A +F++H VR IVG L VG S + +L AK T A+ A A GL L V
Sbjct: 188 IKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYP 247
Query: 353 -KYDLPE 358
+YDLP+
Sbjct: 248 DRYDLPK 254
>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 = 114 bits (284), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 103/304 (33%), Positives = 135/304 (44%), Gaps = 56/304 (18%)
Query: 57 IQRYLIAVEYIGTRFSGSQKQ-LNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAAS 115
++R L+ EY GT F+G Q+Q RTV G LE A P +++ + RTDAGVHA +
Sbjct: 1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVA-AGRTDAGVHALA 59
Query: 116 NVCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQ 175
HVDVE P E +P A+N L D+ V R V DFHAR A
Sbjct: 60 MPFHVDVESAI---PVEKVP--------EALNRLLPE--DLKVVGAREVAPDFHARKDAL 106
Query: 176 ERTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANS 235
R Y YRIL P P S + RA V LDL AM+EA +L+G H+F F +
Sbjct: 107 WRAYRYRILVRPHP-SPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGE 165
Query: 236 PIRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVI 295
R L E ++L + G + + +
Sbjct: 166 --RELLE----------------------------ARLQVAEGEAGL--------EVRLY 187
Query: 296 ARARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYD 355
R +SFL QVR +VG L VG G+ ++ ILK A P APA GL FV+
Sbjct: 188 FRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLY--FVEAA 245
Query: 356 LPED 359
PE+
Sbjct: 246 YPEE 249
>pdb|2XPD|A Chain A, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPD|B Chain B, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPD|C Chain C, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPD|D Chain D, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPD|E Chain E, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPD|F Chain F, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPE|A Chain A, Oxidised Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|2XPE|B Chain B, Oxidised Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|3ZRD|A Chain A, Oxidised Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|3ZRD|B Chain B, Oxidised Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
pdb|3ZRE|A Chain A, Reduced Thiol Peroxidase (Tpx) From Yersinia
Pseudotuberculosis
Length = 200
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 94 FIGQPVSIS-----LSSRTDAGVHAASNVCHVDVERIS-KRKPGEVLPPHDSSVVRRAVN 147
F G PVS++ + + A ++ V + + KRK + P D+ V +V
Sbjct: 40 FQGNPVSVAGKLPQIGDKAKDFTLVAKDLSDVALSSFAGKRKVLNIFPSIDTGVCAASVR 99
Query: 148 HFLQSEGDIMVTDVRCVPSDF---HARFRAQE 176
F Q G++ T V C+ SD +RF E
Sbjct: 100 KFNQLAGELENTVVLCISSDLPFAQSRFCGAE 131
>pdb|2YJH|A Chain A, Thiol Peroxidase From Yersinia Psuedotuberculosis,
Inactive Mutant C61s
Length = 200
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 94 FIGQPVSIS-----LSSRTDAGVHAASNVCHVDVERIS-KRKPGEVLPPHDSSVVRRAVN 147
F G PVS++ + + A ++ V + + KRK + P D+ V +V
Sbjct: 40 FQGNPVSVAGKLPQIGDKAKDFTLVAKDLSDVALSSFAGKRKVLNIFPSIDTGVSAASVR 99
Query: 148 HFLQSEGDIMVTDVRCVPSDF---HARFRAQE 176
F Q G++ T V C+ SD +RF E
Sbjct: 100 KFNQLAGELENTVVLCISSDLPFAQSRFCGAE 131
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 0.132 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,713,991
Number of Sequences: 62578
Number of extensions: 352349
Number of successful extensions: 792
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 777
Number of HSP's gapped (non-prelim): 8
length of query: 382
length of database: 14,973,337
effective HSP length: 101
effective length of query: 281
effective length of database: 8,652,959
effective search space: 2431481479
effective search space used: 2431481479
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)