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= 045140
(468 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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 13/121 (10%)
Query: 60 RKIAIFFAYCGVGYQGMQKNP-GAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
R++ + Y G + G+Q+ G +T++G+LE AL GA+ + + RT
Sbjct: 2 RRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKA----------VAAGRT 51
Query: 119 DKGVSAVGQV--VSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYV 176
D GV A+ V I + E LN LP +++ G + V F+A+K R Y
Sbjct: 52 DAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYR 111
Query: 177 Y 177
Y
Sbjct: 112 Y 112
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 46/107 (42%), Gaps = 5/107 (4%)
Query: 350 LKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIR 409
L +G HNF F K E R ++ G++ ++ G+SF+ Q+R
Sbjct: 144 LSLLLGRHNFLGFA---KEETRPGERELLEARLQVAEGEAGLE-VRLYFRGKSFLRGQVR 199
Query: 410 KMIGLAVAV-VRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIF 455
M+G + V + P+SL D + PTAP GLY E +
Sbjct: 200 GMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAY 246
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 42/139 (30%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 61 KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDK 120
KIA+ Y G Y G Q+ ++++ LE+AL S +E P A RTD
Sbjct: 11 KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL--SQVANE-----PITVFCA--GRTDA 61
Query: 121 GVSAVGQVVSGRFCI--DPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYL 178
GV GQVV +N+NLP I + K V F+A+ RRY Y+
Sbjct: 62 GVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYI 121
Query: 179 LPVFALDSSSHRDRESVMA 197
+ +HR R +V++
Sbjct: 122 I-------YNHRLRPAVLS 133
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 55/122 (45%), Gaps = 7/122 (5%)
Query: 330 LLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVE 389
L KG Y + +R +R + +G ++F +F + + + R ++ V
Sbjct: 132 LSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRA-VQCQSRTPWRNVMHIN----VTRH 186
Query: 390 GIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLI-ETALQKDVNINVPTAPEVGL 448
G ++ ++ +F+ H +R ++G + V + P+S I E KD + TA GL
Sbjct: 187 G-PYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGL 245
Query: 449 YL 450
YL
Sbjct: 246 YL 247
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 42/139 (30%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 61 KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDK 120
KIA+ Y G Y G Q+ ++++ LE+AL S +E P A RTD
Sbjct: 5 KIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL--SQVANE-----PITVFCA--GRTDA 55
Query: 121 GVSAVGQVVSGRFCI--DPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYL 178
GV GQVV +N+NLP I + K V F+A+ RRY Y+
Sbjct: 56 GVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYI 115
Query: 179 LPVFALDSSSHRDRESVMA 197
+ +HR R +V++
Sbjct: 116 I-------YNHRLRPAVLS 127
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 55/122 (45%), Gaps = 7/122 (5%)
Query: 330 LLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVE 389
L KG Y + +R +R + +G ++F +F + + + R ++ V
Sbjct: 126 LSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRA-VQCQSRTPWRNVMHIN----VTRH 180
Query: 390 GIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLI-ETALQKDVNINVPTAPEVGL 448
G ++ ++ +F+ H +R ++G + V + P+S I E KD + TA GL
Sbjct: 181 G-PYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGL 239
Query: 449 YL 450
YL
Sbjct: 240 YL 241
>pdb|3UPY|A Chain A, Crystal Structure Of The Brucella Abortus Enzyme
Catalyzing The First Committed Step Of The
Methylerythritol 4-Phosphate Pathway.
pdb|3UPY|B Chain B, Crystal Structure Of The Brucella Abortus Enzyme
Catalyzing The First Committed Step Of The
Methylerythritol 4-Phosphate Pathway
Length = 445
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 13/99 (13%)
Query: 188 SHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVD 247
+ D++ V+ SLG+G+E C+E E + +G Y++ +N LN D
Sbjct: 152 AQADKQGVIYSLGAGDEPSSCMELIE----FVSALG---YEVVSAGKGKNNPLNFDATPD 204
Query: 248 TVVSTCNGDRHNTN----LESVESNKTISESVMVENANS 282
DR N N +E ++ +KT+ E + NA
Sbjct: 205 DYRQ--EADRRNMNVRLLVEFIDGSKTMVEMAAIANATG 241
>pdb|3UPL|A Chain A, Crystal Structure Of The Brucella Abortus Enzyme
Catalyzing The First Committed Step Of The
Methylerythritol 4-Phosphate Pathway.
pdb|3UPL|B Chain B, Crystal Structure Of The Brucella Abortus Enzyme
Catalyzing The First Committed Step Of The
Methylerythritol 4-Phosphate Pathway
Length = 446
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 13/99 (13%)
Query: 188 SHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVD 247
+ D++ V+ SLG+G+E C+E E + +G Y++ +N LN D
Sbjct: 152 AQADKQGVIYSLGAGDEPSSCMELIE----FVSALG---YEVVSAGKGKNNPLNFDATPD 204
Query: 248 TVVSTCNGDRHNTN----LESVESNKTISESVMVENANS 282
DR N N +E ++ +KT+ E + NA
Sbjct: 205 DYRQ--EADRRNMNVRLLVEFIDGSKTMVEMAAIANATG 241
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
0.314 0.130 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,819,293
Number of Sequences: 62578
Number of extensions: 497830
Number of successful extensions: 760
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 751
Number of HSP's gapped (non-prelim): 12
length of query: 468
length of database: 14,973,337
effective HSP length: 102
effective length of query: 366
effective length of database: 8,590,381
effective search space: 3144079446
effective search space used: 3144079446
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)