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= 0001.4124.p
         (306 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313551|ref|YP_003777643.1| ABC transporter permease [Herba...   560   e-161
gi|300310743|ref|YP_003774835.1| ABC transporter permease [Herba...   139   3e-34

>gi|300313551|ref|YP_003777643.1| ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 306

 Score =  560 bits (1444), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 296/306 (96%), Positives = 303/306 (99%)

Query: 1   MEQLAPLIAASINAGTPLLLAAIGLLINERSGVLNLGAEGMMLVSAIAGFAVGYTTKSPL 60
           MEQLAPLIAASINAGTPLLLAAIGLLINERSGVLNLGAEGMMLV+AIAGFAVGYTTKSPL
Sbjct: 1   MEQLAPLIAASINAGTPLLLAAIGLLINERSGVLNLGAEGMMLVAAIAGFAVGYTTKSPL 60

Query: 61  LGFLAGAVCGMLMASLFAWLALQLATNQVATGLALSIFGAGLSAFVGQRFVGLALPAQPN 120
           LGF+AGAVCGMLMA+LFAWLAL+LATNQVATGLALSIFGAGLSAFVGQRFVGLALPAQ  
Sbjct: 61  LGFMAGAVCGMLMATLFAWLALRLATNQVATGLALSIFGAGLSAFVGQRFVGLALPAQST 120

Query: 121 SIPLLGDIPFLGTALFHQHWMSYLAFALCLASIWFLYRTRAGLVLRAVGESPESAHALGY 180
           S+PLLGD+PFLG ALFHQHWMSY+AFALCLASIWFLYRTRAGLVLRAVGESPESAHALGY
Sbjct: 121 SVPLLGDLPFLGQALFHQHWMSYVAFALCLASIWFLYRTRAGLVLRAVGESPESAHALGY 180

Query: 181 SVRGIRYLALLFGGACCGLAGAYMSLVYTPMWVEGLVAGRGWIALALTAFATWRPARVLL 240
           SVRGIRYLALLFGGACCGLAGAYMSLVYTPMWVEGLVAGRGWIALALTAFATWRPARVLL
Sbjct: 181 SVRGIRYLALLFGGACCGLAGAYMSLVYTPMWVEGLVAGRGWIALALTAFATWRPARVLL 240

Query: 241 GSLLFGGVTIAQFYLQGMGVTVPSQILSMAPYLATIVVLALISRNPDWIRLNMPASLGKP 300
           GSLLFGGVTIAQFYLQGMGVTVPSQILSMAPYLATIVVLALISRNPDWIRLNMPASLGKP
Sbjct: 241 GSLLFGGVTIAQFYLQGMGVTVPSQILSMAPYLATIVVLALISRNPDWIRLNMPASLGKP 300

Query: 301 FRPGAS 306
           FRPGAS
Sbjct: 301 FRPGAS 306


>gi|300310743|ref|YP_003774835.1| ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 306

 Score =  139 bits (350), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 109/298 (36%), Positives = 156/298 (52%), Gaps = 15/298 (5%)

Query: 7   LIAASINAGTPLLLAAIGLLINERSGVLNLGAEGMMLVSAIAGFAVGYTTKSPLLGFLAG 66
           L A +I  GTP L  ++G  + E+ G +NLG EG+++  A+ G+A  + + S  LG LA 
Sbjct: 13  LFAGAIRVGTPFLFVSLGECLTEKGGRVNLGLEGILVCGAMTGYAASFYSGSAWLGVLAA 72

Query: 67  AVCGMLMASLFAWLALQLATNQVATGLALSIFGAGLSAFVGQRFVGLALPAQPNSIPLLG 126
              G+L+  L   +      N +A G+AL + G GL+ F+G+ F+      QP + P+L 
Sbjct: 73  GCTGLLLGVLHGVVCSLPRVNDIAFGIALMLLGTGLAFFLGKPFI------QPQA-PMLP 125

Query: 127 DIPF----LGTALFHQHWMSYLAF---ALCLASIWFLYRTRAGLVLRAVGESPESAHALG 179
            I          L H   ++ L F    L L   W L  TR GL LR VG+  E+A ALG
Sbjct: 126 SIDLGAWSSNDRLHHALQINALFFIGVVLALVLQWGLSATRWGLALRLVGDHAETARALG 185

Query: 180 YSVRGIRYLALLFGGACCGLAGAYMSLVYTPMWVEGLVAGRGWIALALTAFATWRPARVL 239
           Y + G R  A   GG    + GAY+SL Y   W EGL +G+G +A+AL  FA W+P R L
Sbjct: 186 YRLTGTRIAATAAGGFLAAVGGAYLSLYYPGSWNEGLSSGQGLMAVALVIFARWQPWRCL 245

Query: 240 LGSLLFGGVTIAQFYLQGMGVTVPSQILSMAPYLATIVVLALISRNPDWIRLNMPASL 297
           L +LLFG        LQ +GVT    + + APY  T++++ +  R PD    + P  L
Sbjct: 246 LAALLFGAAGALGPALQAVGVTSGYYLFNAAPYALTLLIMIMTCR-PDRTLSSAPGEL 302


  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
   0.327    0.140    0.434 

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: 1,002,142
Number of extensions: 42694
Number of successful extensions: 301
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 5
Length of query: 306
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 221
Effective length of database: 1,217,395
Effective search space: 269044295
Effective search space used: 269044295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 130 (54.7 bits)