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= 005677
         (683 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 =  127 bits (320), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 89/276 (32%), Positives = 151/276 (54%), Gaps = 17/276 (6%)

Query: 110 PAQSELSTQLQQKAQQPHSVSRSDEERVLISEVLVRNKDGEELERKDLETEALTALKACR 169
           PA +  +T   +    P++   + E RVL+SEVLVR + G+     +LET+    ++  +
Sbjct: 35  PAPAPGTTPGTENFNTPNATPETTEPRVLVSEVLVRPQSGQLT--PELETQVYNVIR-TQ 91

Query: 170 ANSALTVREVQEDVHRIIDSGYFCSCMPVAVDTRDGIRLVFQVEPNQEFHGLVCE---GA 226
                T  ++QED++ I  +G+F +      DT  G+R+ F V+PN     +  +   G 
Sbjct: 92  PGRTTTRSQLQEDINAIFGTGFFSNVQASPEDTPLGVRVSFIVQPNPVLSKVEIQANPGT 151

Query: 227 NV---LPTKFVEDAFRDGYGKVVNIRRLDEVITSINGWYMERG--LFGMVSGVEILSGGI 281
           NV   LP    ++ FR  YGK++N+R L E I  +   Y ++G  L  +V   ++   G+
Sbjct: 152 NVPSVLPQATADEIFRAQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAPQVSENGV 211

Query: 282 IRLQVAEAEVNNISIRFLDRK------TGEPTKGKTRPETILRQLTTKKGQVYSMLQGKR 335
           + LQVAE  V NIS+RF +++       G+P +G+T+   I R++  K GQV++    ++
Sbjct: 212 VTLQVAEGVVENISVRFRNKEGQDVNEQGQPIRGRTQDYIITREVELKPGQVFNRNTVQK 271

Query: 336 DVETVLTMGIMEDVSIIPQPAGDTGKVDLIMNVVER 371
           D++ V   G+ EDV++   P  D  KV++++NVVER
Sbjct: 272 DLQRVFGTGLFEDVNVSLDPGTDPTKVNVVVNVVER 307


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

 Score =  119 bits (297), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 79/241 (32%), Positives = 128/241 (53%), Gaps = 10/241 (4%)

Query: 133 DEERVLISEVLVRNKDGEELERKDLETEALTALKACRANSALTVREVQEDVHRIIDSGYF 192
           DE +VLI+EV+V   +G   E + L  + +    + R  S  T  ++Q+D + I  +G+F
Sbjct: 1   DEPKVLIAEVVV---EGATPELEQLVYQVI----STRPGSTTTRTQLQQDTNAIFATGFF 53

Query: 193 CSCMPVAVDTRDGIRLVFQVEPNQEFHGLVCEGANVLPTKFVEDAFRDGYGKVVNIRRLD 252
                V  DT  G+R+ F V P      +   G  VL  + V + F    G+ +N+R L 
Sbjct: 54  ADVNAVPRDTPLGVRITFVVRPYPVLRAVQVAGNQVLTQEKVNEIFAPQIGRTLNLRELQ 113

Query: 253 EVITSINGWYMERG-LFGMVSGV-EILSGGIIRLQVAEAEVNNISIRFLDRKTGEPTKGK 310
             I  IN +Y + G + G V G  ++   G++ LQVAE  V  ++ RFL+ K GEPTK +
Sbjct: 114 AGIEKINTFYRDNGYILGQVVGTPQVDPDGVVTLQVAEGVVEQVTYRFLN-KEGEPTKQR 172

Query: 311 TRPETILRQLTTKKGQVYSMLQGKRDVETVLTMGIMEDVSIIPQPAGDTGKVDLIMNVVE 370
           TR   I R++ T+ G V +    + D+  +  +G+ EDV +  +P  +  +V+LI+N+ E
Sbjct: 173 TRDFVISREMDTQPGVVLNQKTVQADLRRLFELGLFEDVQVALEPGQNPRRVNLILNIKE 232

Query: 371 R 371
           R
Sbjct: 233 R 233


>pdb|2NV4|A Chain A, Crystal Structure Of Upf0066 Protein Af0241 In Complex
           With S-Adenosylmethionine. Northeast Structural Genomics
           Consortium Target Gr27
 pdb|2NV4|B Chain B, Crystal Structure Of Upf0066 Protein Af0241 In Complex
           With S-Adenosylmethionine. Northeast Structural Genomics
           Consortium Target Gr27
          Length = 147

 Score = 32.0 bits (71), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 11/83 (13%)

Query: 236 DAFRDGYGKVVNIRRL-----------DEVITSINGWYMERGLFGMVSGVEILSGGIIRL 284
           D + DG  K+ N+R +           D++     G   ERG+F   S       G+  +
Sbjct: 36  DEYADGLHKIENLRHIIVLYWXDKASRDKLRVVPPGETEERGVFTTRSPSRPNPIGLCVV 95

Query: 285 QVAEAEVNNISIRFLDRKTGEPT 307
           ++ E E N + +R+LD   G P 
Sbjct: 96  EILEVERNRLKVRWLDALDGSPV 118


  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    0.134    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,605,691
Number of Sequences: 62578
Number of extensions: 679233
Number of successful extensions: 1394
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1384
Number of HSP's gapped (non-prelim): 8
length of query: 683
length of database: 14,973,337
effective HSP length: 105
effective length of query: 578
effective length of database: 8,402,647
effective search space: 4856729966
effective search space used: 4856729966
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: 55 (25.8 bits)