BLASTP 2.2.18 [Mar-02-2008]


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= 0004.0002.p
         (550 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310312|ref|YP_003774404.1| hypothetical protein Hsero_0979...   163   4e-41

>gi|300310312|ref|YP_003774404.1| hypothetical protein Hsero_0979
           [Herbaspirillum seropedicae SmR1]
          Length = 613

 Score =  163 bits (412), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 144/445 (32%), Positives = 215/445 (48%), Gaps = 48/445 (10%)

Query: 62  LTRNELTSL-ANTIADKLVGQAYQWNKERNDAETPKTDDPVLLARAKQATESIYGKASNP 120
           +TR  L +L A  +A +   +A Q      DAE P + +P  LARA+QATES+YG+A+NP
Sbjct: 96  VTRKLLFALEAQLVAARGSAEAIQLA----DAELPPSQEPQRLARARQATESLYGRAANP 151

Query: 121 FLGLSRDQLAIIAYDEGGPFTVNERSAAWLEASRQEYEWRKQIMSRSQDAYHRTGNSNAE 180
           F GL R +L+ I YD+ G +T+NER AA  + +  +  +   +  R+ +      + N +
Sbjct: 152 FAGLGRAELSAIVYDDSGAYTINERYAAANQRTELDQRFWAPVFQRALE------SGNWQ 205

Query: 181 GVAQEMLDHYKGLPAIEQSLYPRSYESELQVLIATSGQDQRSSIKLESMNLLTLLNKWAK 240
            V    L  Y  L A+E++ YP +Y   LQ             + L  +    +L    +
Sbjct: 206 PVITAALVFYVSLSALERTAYPDNYPQLLQ-----------QYLDLYRLQPQAVLPAPQQ 254

Query: 241 ARAEHGLPTLDGSGDDSAKSKIAAAAISG-----TGPDSGRIDEVAP-IAPQVEA-TPAD 293
           A     L TL   G   A   +A  AI G      GP    I   AP +A  V+    A 
Sbjct: 255 ADLARMLETLVLPGGPLA---LAGGAIQGLLLPRLGPSLAEILAAAPRLADLVQVNNLAH 311

Query: 294 KTNVDSYSIMLKRVFGASDQKHEPAVTTKATLGSN-----------PRDFLTAEDRKFLA 342
                SY ++L+RVFG   ++ EPA   + ++  N            RDFL+  DR++LA
Sbjct: 312 SVQDSSYLLLLQRVFGVQRREDEPAPARRTSVPGNGSGVGNMAALAARDFLSYGDRRYLA 371

Query: 343 RTYEFAAQTGSAPEDVDGLAFDLAHFRFMQATGNNIENKPGMIWNTDGSPLYYRMTEDDT 402
             Y +A Q G APE+VD LA DLA +R  +A      +          +    RM+ +D 
Sbjct: 372 AAYAYAQQQGIAPEEVDALAQDLARYRQERAGAGASADAADAARALAHT---TRMSSEDR 428

Query: 403 TVATRILKSQSAATTSIDHGFIAYITNPRGIGWTNESNRGHATSLSFLEKLINAGAAEPL 462
            +A R+L SQ+A  T +DH F+A++ +P G GW +    GH+ SL  LE+L+   A   L
Sbjct: 429 LIAQRLLSSQAARQTQLDHAFLAWLLDPAGGGWRDGLASGHSVSLGVLERLLAGLAGVSL 488

Query: 463 AEVAPDSIELN--YKNSLSSIERQD 485
            + A  + EL   Y+  L  I  Q+
Sbjct: 489 GQSAGPAAELEPAYRLVLERIALQE 513


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.312    0.127    0.362 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,634,126
Number of extensions: 64330
Number of successful extensions: 169
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 1
Length of query: 550
Length of database: 1,619,870
Length adjustment: 90
Effective length of query: 460
Effective length of database: 1,193,720
Effective search space: 549111200
Effective search space used: 549111200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 133 (55.8 bits)