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= 0003.0062.p
         (318 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313089|ref|YP_003777181.1| glycerol-3-phosphate ABC transp...   569   e-163
gi|300311925|ref|YP_003776017.1| glycerol-3-phosphate ABC transp...   168   5e-43
gi|300312387|ref|YP_003776479.1| sugar ABC transporter periplasm...    88   1e-18

>gi|300313089|ref|YP_003777181.1| glycerol-3-phosphate ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 437

 Score =  569 bits (1466), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 272/276 (98%), Positives = 274/276 (99%)

Query: 1   MNMMKTLIATGVLATITSSAFAATEITWWHSMTGALGERVNALADDFNKTQGDYKIVPVY 60
           MNMMKTLIATGVLATITSSAFAAT ITWWHSMTGALGERVNALADDFNKTQGDYKIVPVY
Sbjct: 1   MNMMKTLIATGVLATITSSAFAATAITWWHSMTGALGERVNALADDFNKTQGDYKIVPVY 60

Query: 61  KGTYDESMSAAIAAYRAGNAPSILQVFEVGTATMIYAKGAVKPVYEVMQQAGEKFDQNAY 120
           KGTYDESMSAAIAAYRAGNAP+ILQVFEVGTATMIYAKGAVKPVYEVM QAGEKFDQNAY
Sbjct: 61  KGTYDESMSAAIAAYRAGNAPAILQVFEVGTATMIYAKGAVKPVYEVMHQAGEKFDQNAY 120

Query: 121 VPAVAGYYSTPKGMMSFPFNSSTTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKAS 180
           VPAVAGYYSTPKGMMSFPFNSSTTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKAS
Sbjct: 121 VPAVAGYYSTPKGMMSFPFNSSTTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKAS 180

Query: 181 GASCAYTTTWQSWVHLESFSTWHNVELATKNNGFGGLDARLKMNSPLHVRHIENLSNWAK 240
           GA+CAYTTTWQSWVHLESFSTWHNVELATKNNGFGGLDARLKMNSPLHVRHIENLSNWAK
Sbjct: 181 GAACAYTTTWQSWVHLESFSTWHNVELATKNNGFGGLDARLKMNSPLHVRHIENLSNWAK 240

Query: 241 QGYFTYAGRKDEANAKFNAGECAIITGSSSAYADIR 276
           QGYFTYAGRKDEANAKFNAGECAIITGSSSAYADIR
Sbjct: 241 QGYFTYAGRKDEANAKFNAGECAIITGSSSAYADIR 276


>gi|300311925|ref|YP_003776017.1| glycerol-3-phosphate ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 452

 Score =  168 bits (425), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 93/293 (31%), Positives = 148/293 (50%), Gaps = 14/293 (4%)

Query: 23  ATEITWWHSMTGALGERVNALADDFNKTQGDYKIVPVYKGTYDESMSAAIAAYRAGNAPS 82
           A    +W S  GA+ + V  L   FN  Q  +++  V  GTY+++M   IA YRA   P+
Sbjct: 37  AASFEFWSSHAGAMAQAVRQLCAGFNAAQQQHQVRCVVPGTYEQTMQKTIATYRAAQQPA 96

Query: 83  ILQVFEVGTATMIYAKGAVKPVYEVMQQAGEKFDQNAYVPAVAGYYSTPKGMM-SFPFNS 141
           ++++++VGT  M+ + GA+ PV+++M   G + D   Y+PA+ GYY+  +G   S PFN 
Sbjct: 97  LVEIYDVGTLDMMLS-GAIVPVHQLMADHGYRVDWQDYLPAIRGYYTDAQGQFDSLPFNV 155

Query: 142 STTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKASGASCAYTTTWQSWVHLESFST 201
           ST +++ N D   +AG+     P TW+E    A +++A+G +C   + +  W+ LE  ST
Sbjct: 156 STAVLYLNTDQLRQAGI--STLPSTWRELEQTARQLRAAGQTCPLVSDFNPWILLEQVST 213

Query: 202 WHNVELATKNNGFGGLDARLKMNSPLHVRHIENLSNWAKQGYFTYAG--RKDEANAKFNA 259
                +A  +NG  GL A    +  LH+R ++ L  W +Q     A   R       F  
Sbjct: 214 IEGAPIADHDNGHQGLAAHYLFDQGLHLRFMQQLQRWHQQHLLVEAAATRTGRHTLAFTT 273

Query: 260 GECAIITGSSSAYADIRGGGGGISARTPSSSLAWPPCRITTTCRAHRRTPSSA 312
           GECA++  S+SA+  I        AR+    +A  P  I    + H   P  A
Sbjct: 274 GECAMLFDSTSAWHAI--------ARSGLPHVAVRPLPIHADGQRHNSVPGGA 318


>gi|300312387|ref|YP_003776479.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 430

 Score = 87.8 bits (216), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 57/200 (28%), Positives = 95/200 (47%), Gaps = 24/200 (12%)

Query: 25  EITWWHSMT--GALGERVNALADDFNKTQGDYKIVPVYKGTYDESMSAAIAAYRAGNAPS 82
           EI++++ +   GA+ + ++++  DF K   D K+  +Y GTY ES+  A+ A++ G  P+
Sbjct: 29  EISFYYPVAVGGAVTKTIDSMVADFEKAHPDIKVKAIYAGTYQESIVKALTAFKGGTPPT 88

Query: 83  ILQVFEVGTATMIYAKGAVKPVYEVMQQAGEKFDQNAYVPAVAGYYSTPKGMMS------ 136
           +  +      T+I  + A+ P+  +   A +K         +AG+Y   KG M       
Sbjct: 89  LAVLLSTDLFTLI-DENAILPIDSLASSAEDK-------KWIAGFY---KGFMENSQTEG 137

Query: 137 ----FPFNSSTTIMFYNKDMFAKAGLDPEKPPVTWQEFVGMAAKIKASGASCAYTTTWQS 192
                PF  ST +M+YNK +F +AGL+P+K P  W E V  A K+    A     T W  
Sbjct: 138 KTWGIPFQRSTIVMYYNKALFKEAGLNPDKAPANWNEMVEAAKKLTKRDA-AGNVTQWGV 196

Query: 193 WVHLESFSTWHNVELATKNN 212
            +    F  W    +   N+
Sbjct: 197 KIPSTGFGYWMFQAMTASND 216


  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
   0.316    0.128    0.395 

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: 1,023,990
Number of extensions: 43492
Number of successful extensions: 128
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 3
Length of query: 318
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 233
Effective length of database: 1,217,395
Effective search space: 283653035
Effective search space used: 283653035
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 130 (54.7 bits)