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= psy4937
(356 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 35.0 bits (79), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 292 VVIRIPMPARSLLVLWGEARYEWQHCV 318
+ + + +P RSLLV+ GE+RY W H +
Sbjct: 244 IAVPVMLPRRSLLVMTGESRYLWTHGI 270
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 292 VVIRIPMPARSLLVLWGEARYEWQHCV 318
+ + + +P RSLLV GE+RY W H +
Sbjct: 244 IAVPVXLPRRSLLVXTGESRYLWTHGI 270
>pdb|3AXS|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
Aquifex Aeolicus With Sinefungin
pdb|3AXT|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
Aquifex Aeolicus With S-Adenosyl-L-Methionine
Length = 392
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 6 FCGCKGVRTCIKCEQEFGYENKNIVEFTEETYIYCPHCNKAWQGSDLYAYQSHPNHSGKS 65
F +GV K ++FGY YC +C +DLY ++ H G
Sbjct: 225 FVKERGVEKVDKLIEQFGYIQ------------YCFNCMNREVVTDLYKFKEKCPHCGSK 272
Query: 66 FDIGG 70
F IGG
Sbjct: 273 FHIGG 277
>pdb|1TPL|A Chain A, The Three-Dimensional Structure Of Tyrosine Phenol-Lyase
pdb|1TPL|B Chain B, The Three-Dimensional Structure Of Tyrosine Phenol-Lyase
Length = 456
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2TPL|A Chain A, Tyrosine Phenol-lyase From Citrobacter Intermedius Complex
With 3-(4'- Hydroxyphenyl)propionic Acid,
Pyridoxal-5'-phosphate And Cs+ Ion
pdb|2TPL|B Chain B, Tyrosine Phenol-lyase From Citrobacter Intermedius Complex
With 3-(4'- Hydroxyphenyl)propionic Acid,
Pyridoxal-5'-phosphate And Cs+ Ion
Length = 456
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2YCN|A Chain A, Y71f Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCN|B Chain B, Y71f Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
Length = 456
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2EZ2|A Chain A, Apo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2EZ2|B Chain B, Apo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2VLF|A Chain A, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Alanine
pdb|2VLF|B Chain B, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Alanine
pdb|2VLH|A Chain A, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Methionine
pdb|2YCT|A Chain A, Tyrosine Phenol-Lyase From Citrobacter Freundii In Complex
With Pyridine N-Oxide And The Quinonoid Intermediate
Formed With L-Alanine
pdb|2YCT|B Chain B, Tyrosine Phenol-Lyase From Citrobacter Freundii In Complex
With Pyridine N-Oxide And The Quinonoid Intermediate
Formed With L-Alanine
Length = 456
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2YCP|A Chain A, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|B Chain B, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|C Chain C, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|D Chain D, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
Length = 456
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2YHK|A Chain A, D214a Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii
pdb|2YHK|B Chain B, D214a Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii
Length = 456
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|2EZ1|A Chain A, Holo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2EZ1|B Chain B, Holo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2VLH|B Chain B, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Methionine
Length = 456
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 19 EQEFGYENKNIVEFTEETYIYCPHCNKAWQ 48
EQE G+ENK+I E E + Y C + +
Sbjct: 227 EQEQGFENKSIAEIVHEMFSYADGCTMSGK 256
>pdb|1JLH|A Chain A, Human Glucose-6-Phosphate Isomerase
pdb|1JLH|B Chain B, Human Glucose-6-Phosphate Isomerase
pdb|1JLH|C Chain C, Human Glucose-6-Phosphate Isomerase
pdb|1JLH|D Chain D, Human Glucose-6-Phosphate Isomerase
Length = 558
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 109 NHSGKSFDIGGVYIKEDFLSEAETEDVMKQLDDLPWDKSQSGRRKQNF-GPKCNFKKQKI 167
NH + + +I D+ TEDVM+ L DL + R++ F G K N+ + +
Sbjct: 38 NHFSLTLNTNHGHILVDYSKNLVTEDVMRMLVDLAKSRGVEAARERMFNGEKINYTEGRA 97
Query: 168 KL 169
L
Sbjct: 98 VL 99
>pdb|1IAT|A Chain A, Crystal Structure Of Human Phosphoglucose
IsomeraseNEUROLEUKINAUTOCRINE MOTILITY FACTORMATURATION
FACTOR
Length = 557
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 109 NHSGKSFDIGGVYIKEDFLSEAETEDVMKQLDDLPWDKSQSGRRKQNF-GPKCNFKKQKI 167
NH + + +I D+ TEDVM+ L DL + R++ F G K N+ + +
Sbjct: 37 NHFSLTLNTNHGHILVDYSKNLVTEDVMRMLVDLAKSRGVEAARERMFNGEKINYTEGRA 96
Query: 168 KL 169
L
Sbjct: 97 VL 98
>pdb|1IRI|A Chain A, Crystal Structure Of Human Autocrine Motility Factor
Complexed With An Inhibitor
pdb|1IRI|B Chain B, Crystal Structure Of Human Autocrine Motility Factor
Complexed With An Inhibitor
pdb|1IRI|C Chain C, Crystal Structure Of Human Autocrine Motility Factor
Complexed With An Inhibitor
pdb|1IRI|D Chain D, Crystal Structure Of Human Autocrine Motility Factor
Complexed With An Inhibitor
pdb|1JIQ|A Chain A, Crystal Structure Of Human Autocrine Motility Factor
pdb|1JIQ|B Chain B, Crystal Structure Of Human Autocrine Motility Factor
pdb|1JIQ|C Chain C, Crystal Structure Of Human Autocrine Motility Factor
pdb|1JIQ|D Chain D, Crystal Structure Of Human Autocrine Motility Factor
pdb|1NUH|A Chain A, The Crystal Structure Of Human Phosphoglucose Isomerase
Complexed With 5-Phosphoarabinonate
Length = 558
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 109 NHSGKSFDIGGVYIKEDFLSEAETEDVMKQLDDLPWDKSQSGRRKQNF-GPKCNFKKQKI 167
NH + + +I D+ TEDVM+ L DL + R++ F G K N+ + +
Sbjct: 38 NHFSLTLNTNHGHILVDYSKNLVTEDVMRMLVDLAKSRGVEAARERMFNGEKINYTEGRA 97
Query: 168 KL 169
L
Sbjct: 98 VL 99
>pdb|2I13|A Chain A, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
pdb|2I13|B Chain B, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
Length = 190
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 45/97 (46%), Gaps = 14/97 (14%)
Query: 21 EFGYEN---KNIVEFTEETYIYCPHCNKAWQGSDLYAYQSHPNHSG----KSFDIGGVYI 73
EFG + + +E E+ Y CP C K++ SD A H+G K + G +
Sbjct: 3 EFGSSSSVAQAALEPGEKPYA-CPECGKSFSRSDHLAEHQR-THTGEKPYKCPECGKSFS 60
Query: 74 KEDFLT----SQTKETYVYCPHCNKAW-QGSDLYAYQ 105
+ LT + T E CP C K++ Q ++L A+Q
Sbjct: 61 DKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQ 97
>pdb|1Z3H|A Chain A, The Exportin Cse1 In Its Cargo-free, Cytoplasmic State
pdb|1Z3H|B Chain B, The Exportin Cse1 In Its Cargo-free, Cytoplasmic State
Length = 968
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 15/79 (18%)
Query: 263 YPDQKSTIVNDLSLNEKSTDSIVNETLSSVVIRIPMPARSLLVLWGEARYEWQHCVLRSD 322
+PD+ T+++DL+ + D + N+ + +V A S+ W + RSD
Sbjct: 117 FPDRWPTLLSDLASRLSNDDMVTNKGVLTV-------AHSIFKRW--------RPLFRSD 161
Query: 323 VIGRRVCIAYREFTAPYMN 341
+ + + FTAP++N
Sbjct: 162 ELFLEIKLVLDVFTAPFLN 180
>pdb|1WA5|C Chain C, Crystal Structure Of The Exportin Cse1p Complexed With Its
Cargo (Kap60p) And Rangtp
Length = 960
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 15/79 (18%)
Query: 263 YPDQKSTIVNDLSLNEKSTDSIVNETLSSVVIRIPMPARSLLVLWGEARYEWQHCVLRSD 322
+PD+ T+++DL+ + D + N+ + +V A S+ W + RSD
Sbjct: 117 FPDRWPTLLSDLASRLSNDDMVTNKGVLTV-------AHSIFKRW--------RPLFRSD 161
Query: 323 VIGRRVCIAYREFTAPYMN 341
+ + + FTAP++N
Sbjct: 162 ELFLEIKLVLDVFTAPFLN 180
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
0.319 0.135 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,276,200
Number of Sequences: 62578
Number of extensions: 484213
Number of successful extensions: 1066
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1050
Number of HSP's gapped (non-prelim): 24
length of query: 356
length of database: 14,973,337
effective HSP length: 100
effective length of query: 256
effective length of database: 8,715,537
effective search space: 2231177472
effective search space used: 2231177472
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: 52 (24.6 bits)