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= 039285
         (813 letters)

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

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



>pdb|3MC8|A Chain A, Potra1-3 Of The Periplasmic Domain Of Omp85 From Anabaena
 pdb|3MC9|A Chain A, Potra1-2 Of The Periplasmic Domain Of Omp85 From Anabaena
 pdb|3MC9|B Chain B, Potra1-2 Of The Periplasmic Domain Of Omp85 From Anabaena
          Length = 316

 Score = 63.5 bits (153), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/266 (24%), Positives = 115/266 (43%), Gaps = 50/266 (18%)

Query: 167 LSEILFFDRQRGATVGTEDSFFEMVSLRPGGVYTRTQLLKELETLATCGMFEKVDMEAKT 226
           +SE+L   +    T   E   + ++  +PG   TR+QL +++  +   G F  V    + 
Sbjct: 64  VSEVLVRPQSGQLTPELETQVYNVIRTQPGRTTTRSQLQEDINAIFGTGFFSNVQASPED 123

Query: 227 KPDGTLGLTISFLESTWQSAERIRCINVGLMQQSKPIEMDADMTEREKLEYYQSQEKDYK 286
            P   LG+ +SF+                   Q  P+          K+E   +   +  
Sbjct: 124 TP---LGVRVSFIV------------------QPNPV--------LSKVEIQANPGTNV- 153

Query: 287 RRIDKARPCLLPQSVHNEILQILKDHGKV-SARLLQRIRDRVQKWYHDEGYACAQVVNFG 345
                  P +LPQ+  +EI +    +GK+ + R LQ     + K Y D+GY  A VV   
Sbjct: 154 -------PSVLPQATADEIFR--AQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAP 204

Query: 346 NLNTREVVC-EVVEGDITQLVVQFQDK-------LGNVVEGNTQLAVVKRELPKQLRQGN 397
            ++   VV  +V EG +  + V+F++K        G  + G TQ  ++ RE+  +L+ G 
Sbjct: 205 QVSENGVVTLQVAEGVVENISVRFRNKEGQDVNEQGQPIRGRTQDYIITREV--ELKPGQ 262

Query: 398 VFNIEAGKQALRNINSLSLFSNIEVN 423
           VFN    ++ L+ +    LF ++ V+
Sbjct: 263 VFNRNTVQKDLQRVFGTGLFEDVNVS 288


>pdb|2X8X|X Chain X, Structure Of The N-Terminal Domain Of Omp85 From The
           Thermophilic Cyanobacterium Thermosynechococcus
           Elongatus
          Length = 235

 Score = 60.1 bits (144), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 62/255 (24%), Positives = 103/255 (40%), Gaps = 53/255 (20%)

Query: 178 GATVGTEDSFFEMVSLRPGGVYTRTQLLKELETLATCGMFEKVDMEAKTKPDGTLGLTIS 237
           GAT   E   ++++S RPG   TRTQL ++   +   G F  V+   +  P   LG+ I+
Sbjct: 14  GATPELEQLVYQVISTRPGSTTTRTQLQQDTNAIFATGFFADVNAVPRDTP---LGVRIT 70

Query: 238 FLESTWQSAERIRCINVGLMQQSKPIEMDADMTEREKLEYYQSQEKDYKRRIDKARPCLL 297
           F+   +     ++     ++ Q K  E+ A    R                         
Sbjct: 71  FVVRPYPVLRAVQVAGNQVLTQEKVNEIFAPQIGR------------------------- 105

Query: 298 PQSVHNEILQILKDHGKVSARLLQRIRDRVQKWYHDEGYACAQVVNFGNLNTREVVC-EV 356
                            ++ R LQ   +++  +Y D GY   QVV    ++   VV  +V
Sbjct: 106 ----------------TLNLRELQAGIEKINTFYRDNGYILGQVVGTPQVDPDGVVTLQV 149

Query: 357 VEGDITQLVVQFQDKLGNVVEGNTQLAVVKRELPKQLRQGNVFNIEAGKQALRNINSLSL 416
            EG + Q+  +F +K G   +  T+  V+ RE+  Q   G V N +  +  LR +  L L
Sbjct: 150 AEGVVEQVTYRFLNKEGEPTKQRTRDFVISREMDTQ--PGVVLNQKTVQADLRRLFELGL 207

Query: 417 FSNIEV------NPR 425
           F +++V      NPR
Sbjct: 208 FEDVQVALEPGQNPR 222


>pdb|3I45|A Chain A, Crystal Structure Of Putative Twin-Arginine Translocation
           Pathway Signal Protein From Rhodospirillum Rubrum Atcc
           11170
          Length = 387

 Score = 30.8 bits (68), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 4/57 (7%)

Query: 388 ELPKQLRQGNVFNIEAGKQALRNINSLSLFSNIEVNPRPDEKNEGGIIVEIKLKELD 444
           +LPK +R+G V  + AG+Q +  +     +    +NP  DE  EG I+      ++D
Sbjct: 211 DLPKFVREGRVRGLFAGRQVVSMLTGEPEY----LNPLKDEAPEGWIVTGYPWYDID 263


  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    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,853,409
Number of Sequences: 62578
Number of extensions: 996294
Number of successful extensions: 2178
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: 2170
Number of HSP's gapped (non-prelim): 8
length of query: 813
length of database: 14,973,337
effective HSP length: 107
effective length of query: 706
effective length of database: 8,277,491
effective search space: 5843908646
effective search space used: 5843908646
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: 56 (26.2 bits)