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= 044454
         (286 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3BPU|A Chain A, Crystal Structure Of The 3rd Pdz Domain Of Human Membrane
           Associated Guanylate Kinase, C677s And C709s Double
           Mutant
          Length = 88

 Score = 32.3 bits (72), Expect = 0.34,   Method: Composition-based stats.
 Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)

Query: 188 IEIVSMPLNFYYTAADDPGGGFRFVGQ--DNPYS 219
           + IV  P+ F +T AD PGGG + V Q  D+P S
Sbjct: 7   VHIVKGPMGFGFTIADSPGGGGQRVKQIVDSPRS 40


>pdb|3K92|A Chain A, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
 pdb|3K92|B Chain B, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
 pdb|3K92|C Chain C, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
 pdb|3K92|D Chain D, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
 pdb|3K92|E Chain E, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
 pdb|3K92|F Chain F, Crystal Structure Of A E93k Mutant Of The Majour Bacillus
           Su Glutamate Dehydrogenase Rocg
          Length = 424

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 18/33 (54%)

Query: 233 NVGGKQISPSDDTGGMYRTWEMDDPYLTDARPS 265
           + G K I  SD  GG+Y    +D PYL D R S
Sbjct: 242 DAGAKVIGISDANGGLYNPDGLDIPYLLDKRDS 274


>pdb|1T77|A Chain A, Crystal Structure Of The Ph-Beach Domains Of Human LrbaBGL
 pdb|1T77|B Chain B, Crystal Structure Of The Ph-Beach Domains Of Human LrbaBGL
 pdb|1T77|C Chain C, Crystal Structure Of The Ph-Beach Domains Of Human LrbaBGL
 pdb|1T77|D Chain D, Crystal Structure Of The Ph-Beach Domains Of Human LrbaBGL
          Length = 414

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 69  SAPKSTIVTENKQVPYSKSRVSHSQFTYIFNVTAGQKFIRLHFYPSPKPGFNTXXXXXXX 128
           ++P+      N    +    +S+ ++    N  AG+ +  L+ YP   P   T       
Sbjct: 125 ASPRQLFKASNMTQRWQHREISNFEYLMFLNTIAGRSYNDLNQYPV-FPWVITNYESEEL 183

Query: 129 XXXXXTLLRNFSASLAAYGNDRSPFFKEFCINIEDDQ 165
                T  R+ S  + A    R+ FF E   + EDDQ
Sbjct: 184 DLTLPTNFRDLSKPIGALNPKRAAFFAERYESWEDDQ 220


>pdb|1CE8|A Chain A, Carbamoyl Phosphate Synthetase From Escherichis Coli With
            Complexed With The Allosteric Ligand Imp
 pdb|1CE8|C Chain C, Carbamoyl Phosphate Synthetase From Escherichis Coli With
            Complexed With The Allosteric Ligand Imp
 pdb|1CE8|E Chain E, Carbamoyl Phosphate Synthetase From Escherichis Coli With
            Complexed With The Allosteric Ligand Imp
 pdb|1CE8|G Chain G, Carbamoyl Phosphate Synthetase From Escherichis Coli With
            Complexed With The Allosteric Ligand Imp
 pdb|1M6V|A Chain A, Crystal Structure Of The G359f (Small Subunit) Point Mutant
            Of Carbamoyl Phosphate Synthetase
 pdb|1M6V|C Chain C, Crystal Structure Of The G359f (Small Subunit) Point Mutant
            Of Carbamoyl Phosphate Synthetase
 pdb|1M6V|E Chain E, Crystal Structure Of The G359f (Small Subunit) Point Mutant
            Of Carbamoyl Phosphate Synthetase
 pdb|1M6V|G Chain G, Crystal Structure Of The G359f (Small Subunit) Point Mutant
            Of Carbamoyl Phosphate Synthetase
          Length = 1073

 Score = 28.9 bits (63), Expect = 3.8,   Method: Composition-based stats.
 Identities = 9/25 (36%), Positives = 18/25 (72%)

Query: 83   PYSKSRVSHSQFTYIFNVTAGQKFI 107
            P+ + R+ + ++TYI N T+G++ I
Sbjct: 999  PHIQDRIKNGEYTYIINTTSGRRAI 1023


>pdb|1JDB|B Chain B, Carbamoyl Phosphate Synthetase From Escherichia Coli
 pdb|1JDB|E Chain E, Carbamoyl Phosphate Synthetase From Escherichia Coli
 pdb|1JDB|H Chain H, Carbamoyl Phosphate Synthetase From Escherichia Coli
 pdb|1JDB|K Chain K, Carbamoyl Phosphate Synthetase From Escherichia Coli
 pdb|1BXR|A Chain A, Structure Of Carbamoyl Phosphate Synthetase Complexed With
            The Atp Analog Amppnp
 pdb|1BXR|C Chain C, Structure Of Carbamoyl Phosphate Synthetase Complexed With
            The Atp Analog Amppnp
 pdb|1BXR|E Chain E, Structure Of Carbamoyl Phosphate Synthetase Complexed With
            The Atp Analog Amppnp
 pdb|1BXR|G Chain G, Structure Of Carbamoyl Phosphate Synthetase Complexed With
            The Atp Analog Amppnp
 pdb|1C30|A Chain A, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
            Subunit Mutation C269s
 pdb|1C30|C Chain C, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
            Subunit Mutation C269s
 pdb|1C30|E Chain E, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
            Subunit Mutation C269s
 pdb|1C30|G Chain G, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
            Subunit Mutation C269s
 pdb|1C3O|A Chain A, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
            Small Subunit Mutant C269s With Bound Glutamine
 pdb|1C3O|C Chain C, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
            Small Subunit Mutant C269s With Bound Glutamine
 pdb|1C3O|E Chain E, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
            Small Subunit Mutant C269s With Bound Glutamine
 pdb|1C3O|G Chain G, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
            Small Subunit Mutant C269s With Bound Glutamine
 pdb|1CS0|A Chain A, Crystal Structure Of Carbamoyl Phosphate Synthetase
            Complexed At Cys269 In The Small Subunit With The
            Tetrahedral Mimic L-glutamate Gamma-semialdehyde
 pdb|1CS0|C Chain C, Crystal Structure Of Carbamoyl Phosphate Synthetase
            Complexed At Cys269 In The Small Subunit With The
            Tetrahedral Mimic L-glutamate Gamma-semialdehyde
 pdb|1CS0|E Chain E, Crystal Structure Of Carbamoyl Phosphate Synthetase
            Complexed At Cys269 In The Small Subunit With The
            Tetrahedral Mimic L-glutamate Gamma-semialdehyde
 pdb|1CS0|G Chain G, Crystal Structure Of Carbamoyl Phosphate Synthetase
            Complexed At Cys269 In The Small Subunit With The
            Tetrahedral Mimic L-glutamate Gamma-semialdehyde
 pdb|1KEE|A Chain A, Inactivation Of The Amidotransferase Activity Of Carbamoyl
            Phosphate Synthetase By The Antibiotic Acivicin
 pdb|1KEE|C Chain C, Inactivation Of The Amidotransferase Activity Of Carbamoyl
            Phosphate Synthetase By The Antibiotic Acivicin
 pdb|1KEE|E Chain E, Inactivation Of The Amidotransferase Activity Of Carbamoyl
            Phosphate Synthetase By The Antibiotic Acivicin
 pdb|1KEE|G Chain G, Inactivation Of The Amidotransferase Activity Of Carbamoyl
            Phosphate Synthetase By The Antibiotic Acivicin
 pdb|1T36|A Chain A, Crystal Structure Of E. Coli Carbamoyl Phosphate Synthetase
            Small Subunit Mutant C248d Complexed With Uridine
            5'-Monophosphate
 pdb|1T36|C Chain C, Crystal Structure Of E. Coli Carbamoyl Phosphate Synthetase
            Small Subunit Mutant C248d Complexed With Uridine
            5'-Monophosphate
 pdb|1T36|E Chain E, Crystal Structure Of E. Coli Carbamoyl Phosphate Synthetase
            Small Subunit Mutant C248d Complexed With Uridine
            5'-Monophosphate
 pdb|1T36|G Chain G, Crystal Structure Of E. Coli Carbamoyl Phosphate Synthetase
            Small Subunit Mutant C248d Complexed With Uridine
            5'-Monophosphate
          Length = 1073

 Score = 28.9 bits (63), Expect = 3.8,   Method: Composition-based stats.
 Identities = 9/25 (36%), Positives = 18/25 (72%)

Query: 83   PYSKSRVSHSQFTYIFNVTAGQKFI 107
            P+ + R+ + ++TYI N T+G++ I
Sbjct: 999  PHIQDRIKNGEYTYIINTTSGRRAI 1023


>pdb|1A9X|A Chain A, Carbamoyl Phosphate Synthetase: Caught In The Act Of
            Glutamine Hydrolysis
 pdb|1A9X|C Chain C, Carbamoyl Phosphate Synthetase: Caught In The Act Of
            Glutamine Hydrolysis
 pdb|1A9X|E Chain E, Carbamoyl Phosphate Synthetase: Caught In The Act Of
            Glutamine Hydrolysis
 pdb|1A9X|G Chain G, Carbamoyl Phosphate Synthetase: Caught In The Act Of
            Glutamine Hydrolysis
          Length = 1073

 Score = 28.9 bits (63), Expect = 3.8,   Method: Composition-based stats.
 Identities = 9/25 (36%), Positives = 18/25 (72%)

Query: 83   PYSKSRVSHSQFTYIFNVTAGQKFI 107
            P+ + R+ + ++TYI N T+G++ I
Sbjct: 999  PHIQDRIKNGEYTYIINTTSGRRAI 1023


>pdb|1NEP|A Chain A, Crystal Structure Analysis Of The Bovine Npc2
           (Niemann-Pick C2) Protein
 pdb|2HKA|A Chain A, Crystal Structure Of Bovine Npc2 And Cholesterol Sulfate
           Complex
 pdb|2HKA|B Chain B, Crystal Structure Of Bovine Npc2 And Cholesterol Sulfate
           Complex
 pdb|2HKA|C Chain C, Crystal Structure Of Bovine Npc2 And Cholesterol Sulfate
           Complex
          Length = 130

 Score = 28.1 bits (61), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 168 LNITFTPSPDYNDSYAFINGIEIVSMPLNFYYTAADDPGGGFRF-VGQDNPYSILNINAL 226
           +N+TFT +     S A ++GI ++ +P+ F    +D    G R  + +D  Y+ +N   +
Sbjct: 38  VNVTFTSNTQSQSSKAVVHGI-VMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPV 96

Query: 227 ATLYRINVGGKQISPSDDTGGMYRTWEM 254
              Y       +   +DD    +  W++
Sbjct: 97  KNEYPSIKVVVEWELTDDKNQRFFCWQI 124


>pdb|3FEC|A Chain A, Crystal Structure Of Human Glutamate Carboxypeptidase Iii
           (GcpiiiNAALADASE II), PSEUDO-Unliganded
 pdb|3FED|A Chain A, The High Resolution Structure Of Human Glutamate
           Carboxypeptidase Iii (GcpiiiNAALADASE II) IN COMPLEX
           WITH A TRANSITION STATE ANALOG OF Glu-Glu
 pdb|3FEE|A Chain A, The High Resolution Structure Of Human Glutamate
           Carboxypeptidase Iii (GcpiiiNAALADASE II) IN COMPLEX
           WITH QUISQUALIC ACID
 pdb|3FF3|A Chain A, The High Resolution Structure Of Human Glutamate
           Carboxypeptidase Iii (GcpiiiNAALADASE II) IN COMPLEX
           WITH L-Glutamate
          Length = 707

 Score = 27.3 bits (59), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 30  YPLAESNIFLACGWLGNTGPPGQTWVGDVNSQYS 63
           +P+  ++  +   +LG   PP ++W G +N  YS
Sbjct: 252 HPIGYNDAEILLRYLGGIAPPDKSWKGALNVSYS 285


  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    0.136    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,165,306
Number of Sequences: 62578
Number of extensions: 378916
Number of successful extensions: 696
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 688
Number of HSP's gapped (non-prelim): 11
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
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: 51 (24.3 bits)