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= 043340
         (327 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 =  134 bits (337), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 95/277 (34%), Positives = 129/277 (46%), Gaps = 60/277 (21%)

Query: 79  AADGTVKLLIKLEDNRLIETVGIPVEDEKGPMRLTACVSSQVGCPLRCSFCATGKGGFSR 138
           ++DGT+K  I + D R +ETV IP +D     R T CVSSQVGC L C FC+T + GF+R
Sbjct: 88  SSDGTIKWAIAVGDQR-VETVYIPEDD-----RATLCVSSQVGCALECKFCSTAQQGFNR 141

Query: 139 NLSSHEIVGQVLAIEEIF-------KHRVTNVVFMGMGEPMLNLKSVLEAHRCLNKDVQI 191
           NL   EI+GQV    +I        +  +TNVV MGMGEP+LNL +V+ A   +  D   
Sbjct: 142 NLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGF 201

Query: 192 G--QRMITISTVGVPNTIKKLAS---------------------------YKLQSTLA-- 220
           G  +R +T+ST GV   + KL                             Y +++ LA  
Sbjct: 202 GLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAV 261

Query: 221 ---IRSAGVNDQXXXXXXXXXXXXXWGRGH-------------HVNLIPFNPIEGSDYQR 264
              +  +  N                G  H              +NLIP+NP  G+ Y R
Sbjct: 262 RRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGR 321

Query: 265 PYKKAVLAFAGALESHKITTSIRQTRGLDASAACGQL 301
                +  F+  L S+  TT +R+TRG D  AACGQL
Sbjct: 322 SSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQL 358


>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 =  130 bits (327), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 94/277 (33%), Positives = 128/277 (46%), Gaps = 60/277 (21%)

Query: 79  AADGTVKLLIKLEDNRLIETVGIPVEDEKGPMRLTACVSSQVGCPLRCSFCATGKGGFSR 138
           ++DGT+K  I + D R +ETV IP +D     R T CVSSQVGC L C FC+T + GF+R
Sbjct: 88  SSDGTIKWAIAVGDQR-VETVYIPEDD-----RATLCVSSQVGCALECKFCSTAQQGFNR 141

Query: 139 NLSSHEIVGQVLAIEEIF-------KHRVTNVVFMGMGEPMLNLKSVLEAHRCLNKDVQI 191
           NL   EI+GQV    +I        +  +TNVV MGMGEP+LNL +V+ A   +  D   
Sbjct: 142 NLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGF 201

Query: 192 G--QRMITISTVGVPNTIKKLAS---------------------------YKLQSTLA-- 220
           G  +R +T+ST GV   + KL                             Y +++ LA  
Sbjct: 202 GLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAV 261

Query: 221 ---IRSAGVNDQXXXXXXXXXXXXXWGRGH-------------HVNLIPFNPIEGSDYQR 264
              +  +  N                G  H              +NLIP+NP  G+ Y R
Sbjct: 262 RRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGR 321

Query: 265 PYKKAVLAFAGALESHKITTSIRQTRGLDASAACGQL 301
                +  F+  L S+  TT +R+TRG D  AA GQL
Sbjct: 322 SSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAAXGQL 358


>pdb|2CH7|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of A Bacterial
           Chemoreceptor From Thermotoga Maritima
          Length = 309

 Score = 31.6 bits (70), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 151 AIEEIFK--HRVTNVVFMGMGEPMLNLKSVLEAHRCLNKDVQIGQRMITISTVGVPNTIK 208
           +IEEI K    +TN   +G+ + M N+ + +E+     ++   G   I+ +T  + ++ +
Sbjct: 17  SIEEISKANEEITNQ-LLGISKEMDNISTRIESISASVQETTAGSEEISSATKNIADSAQ 75

Query: 209 KLASYKLQSTLAIRSAG 225
           + AS+  QST   + AG
Sbjct: 76  QAASFADQSTQLAKEAG 92


>pdb|2CH7|B Chain B, Crystal Structure Of The Cytoplasmic Domain Of A Bacterial
           Chemoreceptor From Thermotoga Maritima
          Length = 309

 Score = 31.6 bits (70), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 151 AIEEIFK--HRVTNVVFMGMGEPMLNLKSVLEAHRCLNKDVQIGQRMITISTVGVPNTIK 208
           +IEEI K    +TN   +G+ + M N+ + +E+     ++   G   I+ +T  + ++ +
Sbjct: 17  SIEEISKANEEITNQ-LLGISKEMDNISTRIESISASVQETTAGSEEISSATKNIADSAQ 75

Query: 209 KLASYKLQSTLAIRSAG 225
           + AS+  QST   + AG
Sbjct: 76  QAASFADQSTQLAKEAG 92


  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
   0.323    0.137    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,302,229
Number of Sequences: 62578
Number of extensions: 301603
Number of successful extensions: 491
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 8
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)