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= 0004.0033.p
         (317 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA lig...   454   e-129
gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid li...   103   2e-23

>gi|300310928|ref|YP_003775020.1| medium-chain-fatty-acid CoA ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 545

 Score =  454 bits (1169), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 238/322 (73%), Positives = 258/322 (80%), Gaps = 32/322 (9%)

Query: 6   IDTTPEAYGYPLLIKQLLHSSMATAPDQEIVYGIDNQRRHTYADLNVRIQRLGNMLRELG 65
           I  TP AYGYPLLIKQLLHS++ATA  QEI+YG   QRR +YA    R+QRL N L+E+G
Sbjct: 5   IHQTPSAYGYPLLIKQLLHSALATASGQEIIYG---QRRLSYAGFYERVQRLANALKEMG 61

Query: 66  LQRGNTVAVMDWDSHRYLECFFAVPMLGCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSD 125
           LQ GNTVAVMDWDS+RYLECFFAVPM+GCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSD
Sbjct: 62  LQPGNTVAVMDWDSNRYLECFFAVPMMGCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSD 121

Query: 126 FMPILKQIRGELKTLTRCVLITDDX-----------------------------DENARA 156
           F+P+LKQIRGEL TLTRCV +TDD                              DENARA
Sbjct: 122 FLPLLKQIRGELTTLTRCVWLTDDATPCPRGPGFAGEYEELLAQAEPACDFPDFDENARA 181

Query: 157 TTFYTTGTTGLPKGVYFSHRQLVLHTLAVTAGLALAPQQGRLHRDDVYMPLTPMFHVHAW 216
           TTFYTTGTTGLPKGVYFSHRQLVLHTLA TAGLALAPQQGR HRDDVYMPLTPMFHVHAW
Sbjct: 182 TTFYTTGTTGLPKGVYFSHRQLVLHTLATTAGLALAPQQGRFHRDDVYMPLTPMFHVHAW 241

Query: 217 GLPYVATMAGLKQVYPGRYVPDTILKLIDTEKVTFSHCVPTILHMVLSAPAAKDVDLSKW 276
           GLPYVATMAG+KQVYPGRYVPDTI +LI  EKVTFSHCVPTIL MVL++  A++ DLS W
Sbjct: 242 GLPYVATMAGVKQVYPGRYVPDTICRLIREEKVTFSHCVPTILQMVLTSEQAREADLSGW 301

Query: 277 KMIIGGSAMTSALAXAAANNLI 298
           KMIIGGSAMT +LA  A +  I
Sbjct: 302 KMIIGGSAMTGSLAKMARDRGI 323


>gi|300313986|ref|YP_003778078.1| acyl-CoA synthetase/AMP-acid
           ligase II protein [Herbaspirillum seropedicae SmR1]
          Length = 546

 Score =  103 bits (257), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 121/267 (45%), Gaps = 48/267 (17%)

Query: 36  VYG-----IDNQRRHTYADLNVRIQRLGNMLRELGLQRGNTVAVMDWDSHRYLECFFAVP 90
           VYG     I    R  +     R +RL + L+ LG+ + +TV+ M  ++   +E  F VP
Sbjct: 30  VYGKRTAIIHGALRQDWDQTYRRTRRLASALQGLGVGKNDTVSAMLPNTPAMVEAHFGVP 89

Query: 91  MLGCVLQTVNVRLSPEQIAYTLNHAQADVLLVNSDFMPILKQIRGELKTLTRCVLITDD- 149
           M G VL  +N+RL  E I + L H +A VLL++S+F  + +Q+R +L  L + V + D+ 
Sbjct: 90  MAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFAALAQQLRTQLPAL-KIVEVFDEL 148

Query: 150 -------------------------------XDENARATTFYTTGTTGLPKGVYFSHRQL 178
                                           DE       YT+GTTG PKGV + HR  
Sbjct: 149 GPPPVAGERFGHLEYEALLAGGDEHFDWQMPADEWDAIALNYTSGTTGDPKGVVYHHRGA 208

Query: 179 VLHTLAVTAGLALAPQQGRLHRDDVYMPLTPMFHVHAWGLPY-VATMAGLKQVYPGRYVP 237
            L+ ++          +  L +  VY+   PMFH + W  P+ VA  AG+  V   ++ P
Sbjct: 209 ALNAVSNIL-------EWDLPKHPVYLWTLPMFHCNGWCFPWTVAARAGV-NVCLRKFEP 260

Query: 238 DTILKLIDTEKVTFSHCVPTILHMVLS 264
             +  LI    +T  +C   I+H  L+
Sbjct: 261 KLVFDLIAEHGIT-HYCAAPIVHAALA 286


  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
   0.324    0.136    0.419 

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: 882,601
Number of extensions: 33822
Number of successful extensions: 125
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 4
Length of query: 317
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 232
Effective length of database: 1,217,395
Effective search space: 282435640
Effective search space used: 282435640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 130 (54.7 bits)