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= psy9577
         (354 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 =  343 bits (879), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 169/355 (47%), Positives = 236/355 (66%), Gaps = 13/355 (3%)

Query: 3   NLLDLSPLKFVNYCKELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIK 62
           NLLDL+  +   + K+LGE PFRA Q+ KW++ +   +F++MTD++  LR KLK    I+
Sbjct: 19  NLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEIR 78

Query: 63  APHIMSDQISFDGTRKWIFHVKKNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQG 122
           AP ++ +Q S DGT KW   V    +ETV+IPE +R TLC+S+QVGCA+ C FCST +QG
Sbjct: 79  APEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLCVSSQVGCALECKFCSTAQQG 138

Query: 123 FVRNLTVGEIIGQLWVTEFKLRREKNI-KINSQGKRQITNIVMMGMGEPLLNYKSTIGAL 181
           F RNL V EIIGQ+W      R  K +      G+R ITN+VMMGMGEPLLN  + + A+
Sbjct: 139 FNRNLRVSEIIGQVW------RAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAM 192

Query: 182 KLILSDHAYGLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKY 241
           +++L D  +GLS+R V LSTSG++P +DKL     V LA+SLHA N+ +R+++VPI+KKY
Sbjct: 193 EIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKY 252

Query: 242 PLKELILACHRYITYSPRHM--ITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINL 299
            ++  + A  RY+  S  +   +T EY ML  +ND   HA +L  L++     T CKINL
Sbjct: 253 NIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKD----TPCKINL 308

Query: 300 IPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGKIL 354
           IP+N FP +    S NSRI  F+K+LM+ G    +RK RG+DI+AACGQL+G ++
Sbjct: 309 IPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQLAGDVI 363


>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 =  339 bits (869), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 168/355 (47%), Positives = 235/355 (66%), Gaps = 13/355 (3%)

Query: 3   NLLDLSPLKFVNYCKELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIK 62
           NLLDL+  +   + K+LGE PFRA Q+ KW++ +   +F++MTD++  LR KLK    I+
Sbjct: 19  NLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEIR 78

Query: 63  APHIMSDQISFDGTRKWIFHVKKNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQG 122
           AP ++ +Q S DGT KW   V    +ETV+IPE +R TLC+S+QVGCA+ C FCST +QG
Sbjct: 79  APEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLCVSSQVGCALECKFCSTAQQG 138

Query: 123 FVRNLTVGEIIGQLWVTEFKLRREKNI-KINSQGKRQITNIVMMGMGEPLLNYKSTIGAL 181
           F RNL V EIIGQ+W      R  K +      G+R ITN+VMMGMGEPLLN  + + A+
Sbjct: 139 FNRNLRVSEIIGQVW------RAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAM 192

Query: 182 KLILSDHAYGLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKY 241
           +++L D  +GLS+R V LSTSG++P +DKL     V LA+SLHA N+ +R+++VPI+KKY
Sbjct: 193 EIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKY 252

Query: 242 PLKELILACHRYITYSPRHM--ITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINL 299
            ++  + A  RY+  S  +   +T EY ML  +ND   HA +L  L++     T CKINL
Sbjct: 253 NIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKD----TPCKINL 308

Query: 300 IPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGKIL 354
           IP+N FP +    S NSRI  F+K+LM+ G    +RK RG+DI+AA GQL+G ++
Sbjct: 309 IPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAAXGQLAGDVI 363


  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
   0.325    0.139    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,724,845
Number of Sequences: 62578
Number of extensions: 383792
Number of successful extensions: 924
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 916
Number of HSP's gapped (non-prelim): 3
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)