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= psy12402
(375 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 = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 64/267 (23%), Positives = 112/267 (41%), Gaps = 32/267 (11%)
Query: 1 MAMMFAYSGVGYFGLQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQ 60
+ ++ Y G + GLQ + +G++T++G++ AL G + P+ +
Sbjct: 4 LLLLCEYDGTLFAGLQRQ---------GRGLRTVQGELERALPGIGAL-------PKAVA 47
Query: 61 FQRAARTDKGVSALKQI----VSLKLPEEANKEAINEHLPEQIRILSIKRVTKGFNSKNN 116
A RTD GV AL V +P E EA+N LPE ++++ + V F+++ +
Sbjct: 48 ---AGRTDAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKD 104
Query: 117 CNARTYSYTCPTYAFATP-QDTKDDFRLTPDQFNFLQALLKQYEGTHNFHNFTSKR-KPL 174
R Y Y +P + + P ++ L G HNF F + +P
Sbjct: 105 ALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRP- 163
Query: 175 DPSCSRYIMSFDCEQPFVKDGLELITLKIKGQSFMLHQIRKMVGVAMAIARGFTSKDLIE 234
R ++ + + GLE + L +G+SF+ Q+R MVG + + G + ++
Sbjct: 164 ---GERELLEARLQVAEGEAGLE-VRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLK 219
Query: 235 KTFGLDQFDL--PMAPGLGLLLEQVHY 259
L P AP GL + Y
Sbjct: 220 AILKTADRRLAGPTAPAHGLYFVEAAY 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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 70/299 (23%), Positives = 110/299 (36%), Gaps = 87/299 (29%)
Query: 1 MAMMFAYSGVGYFGLQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQ 60
+A+ Y G Y+G Q R +++++ + +AL + N P I
Sbjct: 12 IALGIEYDGSKYYGWQ----------RQNEVRSVQEKLEKALSQVA-------NEP--IT 52
Query: 61 FQRAARTDKGVSALKQIVSLKLP----EEANKEAINEHLPEQIRILSIKRVTKGFNSKNN 116
A RTD GV Q+V + + A +N +LP I + +K V F+++ +
Sbjct: 53 VFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFS 112
Query: 117 CNARTYSYTCPTYA------------FATPQDTKDDFRLTPDQFNFLQALLKQYEGTHNF 164
AR Y Y + F P D + R Q LL G ++F
Sbjct: 113 ATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAA-------QCLL----GENDF 161
Query: 165 HNFTS----KRKPLDPSCSRYIMSFDCEQ--PFVKDGLELITLKIKGQSFMLHQIRKMVG 218
+F + R P R +M + + P+V + IK +F+ H +R +VG
Sbjct: 162 TSFRAVQCQSRTPW-----RNVMHINVTRHGPYV-------VVDIKANAFVHHMVRNIVG 209
Query: 219 VAMA----------IARGFTSKD-----LIEKTFGL--------DQFDLPMAPGLGLLL 254
M IA +KD K GL D++DLP P L L
Sbjct: 210 SLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFL 268
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 70/299 (23%), Positives = 110/299 (36%), Gaps = 87/299 (29%)
Query: 1 MAMMFAYSGVGYFGLQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQ 60
+A+ Y G Y+G Q R +++++ + +AL + N P I
Sbjct: 6 IALGIEYDGSKYYGWQ----------RQNEVRSVQEKLEKALSQVA-------NEP--IT 46
Query: 61 FQRAARTDKGVSALKQIVSLKLP----EEANKEAINEHLPEQIRILSIKRVTKGFNSKNN 116
A RTD GV Q+V + + A +N +LP I + +K V F+++ +
Sbjct: 47 VFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFS 106
Query: 117 CNARTYSYTCPTYA------------FATPQDTKDDFRLTPDQFNFLQALLKQYEGTHNF 164
AR Y Y + F P D + R Q LL G ++F
Sbjct: 107 ATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAA-------QCLL----GENDF 155
Query: 165 HNFTS----KRKPLDPSCSRYIMSFDCEQ--PFVKDGLELITLKIKGQSFMLHQIRKMVG 218
+F + R P R +M + + P+V + IK +F+ H +R +VG
Sbjct: 156 TSFRAVQCQSRTPW-----RNVMHINVTRHGPYV-------VVDIKANAFVHHMVRNIVG 203
Query: 219 VAMA----------IARGFTSKD-----LIEKTFGL--------DQFDLPMAPGLGLLL 254
M IA +KD K GL D++DLP P L L
Sbjct: 204 SLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFL 262
>pdb|1TRK|A Chain A, Refined Structure Of Transketolase From Saccharomyces
Cerevisiae At 2.0 Angstroms Resolution
pdb|1TRK|B Chain B, Refined Structure Of Transketolase From Saccharomyces
Cerevisiae At 2.0 Angstroms Resolution
pdb|1NGS|A Chain A, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-phosphate
pdb|1NGS|B Chain B, Complex Of Transketolase With Thiamin Diphosphate, Ca2+
And Acceptor Substrate Erythrose-4-phosphate
pdb|1GPU|A Chain A, Transketolase Complex With Reaction Intermediate
pdb|1GPU|B Chain B, Transketolase Complex With Reaction Intermediate
Length = 680
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 15 LQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQFQRAARTDKGVSAL 74
L+SK+ +I Q + +EG +E+ K G+V +D N P I + V A
Sbjct: 515 LESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVAN-PDIILVATGSEVSLSVEAA 573
Query: 75 KQIVS 79
K + +
Sbjct: 574 KTLAA 578
>pdb|1TKA|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKA|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKB|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKB|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKC|A Chain A, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
pdb|1TKC|B Chain B, Specificity Of Coenzyme Binding In Thiamin Diphosphate
Dependent Enzymes: Crystal Structures Of Yeast
Transketolase In Complex With Analogs Of Thiamin
Diphosphate
Length = 678
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 15 LQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQFQRAARTDKGVSAL 74
L+SK+ +I Q + +EG +E+ K G+V +D N P I + V A
Sbjct: 513 LESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVAN-PDIILVATGSEVSLSVEAA 571
Query: 75 KQIVS 79
K + +
Sbjct: 572 KTLAA 576
>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
Length = 1022
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 10/111 (9%)
Query: 126 CPTYAFATPQDTKDDFRLTPDQFNFLQALLKQYEGTHNF----HNFTSKRKPLDPSCSRY 181
C YA D +D + PD+ + + LLK+ HN S K + SR
Sbjct: 445 CNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRA 504
Query: 182 IMSFDCEQPFVKDGLELITLKIKGQSFMLHQIRKMVGVAMAIARGFTSKDL 232
IM E + K + ++G M K++G+ +A GF SK L
Sbjct: 505 IMYE--ETTYSKKKIIDFLSALEGFKVMC----KIIGIMEEVADGFKSKIL 549
>pdb|1AY0|A Chain A, Identification Of Catalytically Important Residues In
Yeast Transketolase
pdb|1AY0|B Chain B, Identification Of Catalytically Important Residues In
Yeast Transketolase
Length = 680
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 15 LQSKYLFFLIFCRNQGMKTIEGDIMEALFKAGFVTEDSFNTPQNIQFQRAARTDKGVSAL 74
L+SK+ +I Q + +EG +E+ K G+V +D N P I + V A
Sbjct: 515 LESKHTPSIIALSRQNLPQLEGSSIESASKGGYVLQDVAN-PDIILVATGSEVSLSVEAA 573
Query: 75 KQIVS 79
K + +
Sbjct: 574 KTLAA 578
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 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,302,857
Number of Sequences: 62578
Number of extensions: 403453
Number of successful extensions: 844
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 840
Number of HSP's gapped (non-prelim): 10
length of query: 375
length of database: 14,973,337
effective HSP length: 100
effective length of query: 275
effective length of database: 8,715,537
effective search space: 2396772675
effective search space used: 2396772675
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)