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= 0003.0028.p
         (291 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310571|ref|YP_003774663.1| transmembrane protein [Herbaspi...   396   e-111
gi|300309508|ref|YP_003773600.1| dinucleotide-utilizing enzyme p...    71   1e-13

>gi|300310571|ref|YP_003774663.1| transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 285

 Score =  396 bits (1018), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 207/279 (74%), Positives = 234/279 (83%), Gaps = 8/279 (2%)

Query: 14  DIDFDRRFGGIARLYGAQGLARFRAAHICVVGVGGVGSWIVEALARSAIGKITMIDLDNL 73
           DID++RRFGG+ARLYGA  L RFR A +CVVGVGGVGSWIVEALARSAIG +T++DLDNL
Sbjct: 9   DIDYERRFGGVARLYGAAALQRFRQARVCVVGVGGVGSWIVEALARSAIGHLTLVDLDNL 68

Query: 74  AESNVNRQIHALTDTLGKAKVTALHERIMQINPYCQVTEIEDFLTPDNVAEMIGEGRFDY 133
           AESNVNRQIHALT TLG+AKVTALHERI QINP C VTE+EDF+ PDNV +M+G  RFDY
Sbjct: 69  AESNVNRQIHALTTTLGQAKVTALHERIRQINPTCVVTEVEDFVDPDNVEKMLGGERFDY 128

Query: 134 VVDAIDNVRAKVALIAYCREHKVPLLTSGGAGGQIDPTRIEIRDLCRTEQEPLLAKVRKR 193
           V+DAIDNV AKVA+IA+CR++ +P++T G AGGQIDPT+IEIRDLCRTEQEPLLAKVRKR
Sbjct: 129 VIDAIDNVPAKVAMIAWCRKNGMPMVTIGSAGGQIDPTQIEIRDLCRTEQEPLLAKVRKR 188

Query: 194 LRAWHKFPRGTKNKFGIDAVFSTEPLRFP---EGEVCEV-DTDDAADGLDTVDADGRKQD 249
           LRA H FPRGTKNKF IDAVFSTEPLRFP   EGE CE+   +D   G D  D+      
Sbjct: 189 LRAQHGFPRGTKNKFHIDAVFSTEPLRFPELAEGEACEIAPAEDIDVGEDAADS----TQ 244

Query: 250 AGVTGLNCAGFGSAMVVTASFGLVAAGFVLRKIVERPDA 288
           AGVTGLNCAGFGSAMVVTASFGLVAA  VL+K+ E+  A
Sbjct: 245 AGVTGLNCAGFGSAMVVTASFGLVAAAHVLKKLAEQAAA 283


>gi|300309508|ref|YP_003773600.1| dinucleotide-utilizing enzyme
           protein [Herbaspirillum seropedicae SmR1]
          Length = 254

 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/129 (31%), Positives = 69/129 (53%), Gaps = 2/129 (1%)

Query: 32  GLARFRAAHICVVGVGGVGSWIVEALARSAIGKITMIDLDNLAESNVNRQIHALTDTLGK 91
           G  R    H  V+G GG+GS     LA + +G+IT++D D +  +N+ RQI   T  +G+
Sbjct: 22  GQTRLLQGHALVIGAGGLGSPAAMYLASAGVGRITLVDHDTVDLTNLQRQIMHTTARVGQ 81

Query: 92  AKVTALHERIMQINPYCQVTEIEDFLTPDNVAEMIGEGRFDYVVDAIDNVRAKVALIAYC 151
            KV +  + + QINP  QVT + + +  + +  ++ +   D V+D  DN   + A+   C
Sbjct: 82  PKVESGRQALEQINPGVQVTALAERVEAERLHALVAQA--DVVLDCSDNFATRHAVNRAC 139

Query: 152 REHKVPLLT 160
               VPL++
Sbjct: 140 VAAGVPLVS 148


  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
   0.321    0.138    0.409 

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: 894,510
Number of extensions: 36047
Number of successful extensions: 107
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 2
Length of query: 291
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 207
Effective length of database: 1,222,130
Effective search space: 252980910
Effective search space used: 252980910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 130 (54.7 bits)