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= 028700
         (205 letters)

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

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



>pdb|3RF9|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli
 pdb|3RF9|B Chain B, X-Ray Structure Of Rlmn From Escherichia Coli
          Length = 404

 Score =  140 bits (352), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 79/191 (41%), Positives = 117/191 (61%), Gaps = 7/191 (3%)

Query: 1   MGEPLNNYAALVEAVRIM-TGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59
           MGEPL N   +V A+ IM     F +S +R+T+ST G+V A++K   D+  + LA+SLHA
Sbjct: 178 MGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKL-GDMIDVALAISLHA 236

Query: 60  PVQDVRCQIMPAARAFPLEKLMNALKEYQKNS---QQKIFIEYIMLDGVNDEEQHAHQLG 116
           P  ++R +I+P  + + +E  + A++ Y + S   Q ++ IEY+MLD VND  +HAHQL 
Sbjct: 237 PNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLA 296

Query: 117 KLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGA 176
           +LL+     +NLIP+NP       R SS+ ++  F K+L  SY   T VRK  G DI  A
Sbjct: 297 ELLKDTPCKINLIPWNPFPGAPYGR-SSNSRIDRFSKVLM-SYGFTTIVRKTRGDDIDAA 354

Query: 177 CGQLVVNLPDK 187
           CGQL  ++ D+
Sbjct: 355 CGQLAGDVIDR 365


>pdb|3RFA|A Chain A, X-Ray Structure Of Rlmn From Escherichia Coli In Complex
           With S- Adenosylmethionine
 pdb|3RFA|B Chain B, X-Ray Structure Of Rlmn From Escherichia Coli In Complex
           With S- Adenosylmethionine
          Length = 404

 Score =  135 bits (341), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 78/191 (40%), Positives = 116/191 (60%), Gaps = 7/191 (3%)

Query: 1   MGEPLNNYAALVEAVRIM-TGLPFQVSPKRITVSTVGIVHAINKFHSDLPGLNLAVSLHA 59
           MGEPL N   +V A+ IM     F +S +R+T+ST G+V A++K   D+  + LA+SLHA
Sbjct: 178 MGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKL-GDMIDVALAISLHA 236

Query: 60  PVQDVRCQIMPAARAFPLEKLMNALKEYQKNS---QQKIFIEYIMLDGVNDEEQHAHQLG 116
           P  ++R +I+P  + + +E  + A++ Y + S   Q ++ IEY+MLD VND  +HAHQL 
Sbjct: 237 PNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLA 296

Query: 117 KLLETFQVVVNLIPFNPIGSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGA 176
           +LL+     +NLIP+NP       R SS+ ++  F K+L  SY   T VRK  G DI  A
Sbjct: 297 ELLKDTPCKINLIPWNPFPGAPYGR-SSNSRIDRFSKVLM-SYGFTTIVRKTRGDDIDAA 354

Query: 177 CGQLVVNLPDK 187
            GQL  ++ D+
Sbjct: 355 XGQLAGDVIDR 365


>pdb|3C8F|A Chain A, 4fe-4s-Pyruvate Formate-Lyase Activating Enzyme With
           Partially Disordered Adomet
 pdb|3CB8|A Chain A, 4fe-4s-Pyruvate Formate-Lyase Activating Enzyme In Complex
           With Adomet And A Peptide Substrate
          Length = 245

 Score = 35.4 bits (80), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 86  EYQKNSQQKIFIEYIMLDGVNDEEQHAHQLGKLLETFQVV--VNLIPFNPIG 135
           +Y  N   K++I Y+++ G +D++  AH+LG+       V  + L+P++ +G
Sbjct: 154 KYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELG 205


>pdb|2Y3A|A Chain A, Crystal Structure Of P110beta In Complex With Icsh2 Of
            P85beta And The Drug Gdc-0941
          Length = 1092

 Score = 28.1 bits (61), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 63/184 (34%), Gaps = 35/184 (19%)

Query: 47   DLPGLNLAVSLHAPVQDVRCQI--MPAARAFPLEKLMNALKEYQKNSQQKIFIEYIMLD- 103
            D  GL   VS    + D++     + A  AF  + L+N LKEY         IE   L  
Sbjct: 868  DRSGLIEVVSTSETIADIQLNSSNVAATAAFNKDALLNWLKEYNSGDDLDRAIEEFTLSC 927

Query: 104  ----------GVNDEE---------------QHAHQLGKLLETFQVVVNLIPF----NPI 134
                      G+ D                    H LG     F +    +PF    + I
Sbjct: 928  AGYCVASYVLGIGDRHSDNIMVKKTGQLFHIDFGHILGNFKSKFGIKRERVPFILTYDFI 987

Query: 135  GSVSQFRTSSDDKVSSFQKILRGSYNIRTTVRKQMGQDISGACGQLVVNLPDKISAKSTP 194
              + Q +T + +K   F++    +Y I   +R+     I+     L   LP+  S K   
Sbjct: 988  HVIQQGKTGNTEKFGRFRQCCEDAYLI---LRRHGNLFITLFALMLTAGLPELTSVKDIQ 1044

Query: 195  PVTD 198
             + D
Sbjct: 1045 YLKD 1048


  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
   0.320    0.135    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,492,594
Number of Sequences: 62578
Number of extensions: 202413
Number of successful extensions: 576
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 567
Number of HSP's gapped (non-prelim): 5
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
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: 49 (23.5 bits)