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= 0005.0159.p
         (727 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312085|ref|YP_003776177.1| transporter DNA uptake transmem...   734   0.0  

>gi|300312085|ref|YP_003776177.1| transporter DNA uptake
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 829

 Score =  734 bits (1895), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 398/681 (58%), Positives = 485/681 (71%), Gaps = 41/681 (6%)

Query: 1   MRSAILGFAAGIAFLQMQAQLLPFEGHMALLAAAVLLLLACWRLRDTGARAVWKIVLRIV 60
           MRS I+GFA GI  LQMQAQL   E +   L  A LL    W+         W+  LR+ 
Sbjct: 1   MRSLIIGFAIGIGLLQMQAQLPGLEWYGVGLVLAALLGFTAWKF--------WQPFLRVP 52

Query: 61  LFNLAGLCAGFAWGGLMAQYRLDDALPAAWEGHDVVVVGTIDSLPYRFERGVRFNFNVER 120
           L    G   GF W    A Y LD  LPAAWEGHD+ V+GT+  LP    +G+R+ F+VE+
Sbjct: 53  LLLTCGAWLGFLWAAGFAAYYLDQELPAAWEGHDITVIGTVADLPDHSAQGLRWRFDVEQ 112

Query: 121 VAPQNGGRPPVPQRVALSWY------SPGAFGQAGGESGQAVPDVRPGERWQFTVRLKRP 174
           V  Q G +PPVP R+ALSWY      SP   G+    +  A+PD+RPGERW+  VRLKRP
Sbjct: 113 VVLQGGVKPPVPPRLALSWYGNQRYQSPAEDGEQAAPARLALPDMRPGERWRLKVRLKRP 172

Query: 175 HGNANPHGFDYEAWLLEQNLRATGSVRSDQQSAYK-----NHRLQEFVLTPSNAIEYGRA 229
           HGNANP GFDYE WLL+ ++RATG V     +        N RL+ FV TPS+AI+Y R 
Sbjct: 173 HGNANPGGFDYELWLLQDDVRATGYVVGAPAAPGAPATAINRRLEAFVWTPSHAIDYARG 232

Query: 230 WLRDRIMSALPQQKYAGVIVALVIGDQRAIEQSDWSIFNRTGVGHLVAISGLHITLISGL 289
           WLRD I +ALP   YAGVI ALVIGDQR I Q+DWSIFNRTG+GHL+AISGLHIT+++ L
Sbjct: 233 WLRDGIYAALPGAPYAGVIAALVIGDQRGISQADWSIFNRTGIGHLMAISGLHITMLAAL 292

Query: 290 FGAFSGWLWRRSFFTRAQLPLLLPAPKVAVLAGLAAALVYVLLAGFGVPAQRTLYMLCVV 349
           FG  + WLWRRSFFT AQLPL LPA KVAVLAG+AAAL+YVLL+GFGVPAQRTLYML VV
Sbjct: 293 FGGLASWLWRRSFFTGAQLPLRLPAQKVAVLAGMAAALLYVLLSGFGVPAQRTLYMLIVV 352

Query: 350 GLAYWTGRLTHISYVMSLALAVVLLFDPWALLWPGFWLSFGAVAIILYASAGRIGADVSA 409
           G+A+W GR+  +S VMSLAL +VLL DPWALLWPGFWLSFGAV ++LY S GR+      
Sbjct: 353 GIAFWRGRIVRVSLVMSLALGLVLLLDPWALLWPGFWLSFGAVGLLLYGSVGRM-----Q 407

Query: 410 EPQILTPV--QRHRRPSRLARMRRSLRAGAYTQYVVTLGLLPLTMVLFGQYSLLSPLANA 467
            P+ +     ++H  P+ + R++ +    ++ QY+VTLGL+PLT++LFGQYSL+ P+ANA
Sbjct: 408 PPRAMAAAASRKHWWPALVQRLKEA----SHAQYLVTLGLVPLTVLLFGQYSLIGPIANA 463

Query: 468 VAIPLITLVVAPLSLLGSILPPPLSQWLLLAAHTVLEWLVQWLELLAGQPFAVWQAPLPP 527
           VAIPL++LV+ PL+LLGS+LP  L+Q++L   H +L WL  +L+ L+  P+AVWQ P+P 
Sbjct: 464 VAIPLVSLVITPLALLGSVLPTVLAQFVLQLPHALLAWLAGFLQGLSAMPWAVWQTPVPS 523

Query: 528 LWVFALALGGTLLLLAPLARWLGLFGWLXGWLARWLGLFGWLPLIFNTPTWPEQGQVHVT 587
            W+FALA+GGT+LLLAP            GW  RWLG FGWLPL+ N P  P +G + VT
Sbjct: 524 WWMFALAMGGTMLLLAP-----------RGWPVRWLGWFGWLPLLLNAPMAPAEGSMRVT 572

Query: 588 AFDVGQGMALLVETPGHRLLYDTGPYYSPESDGANRVIVPYLRARGIDHLDAVVISHNDN 647
           AFDVGQGMA+LVETP HRLLYDTGPYY+PESDGA RVI+PYLRARGIDHLD VVISHNDN
Sbjct: 573 AFDVGQGMAVLVETPTHRLLYDTGPYYTPESDGATRVILPYLRARGIDHLDRVVISHNDN 632

Query: 648 DHSGGALSLFKEIARRPARSS 668
           DHSGGALSLF  +      SS
Sbjct: 633 DHSGGALSLFGSLPVDSVYSS 653


  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
   0.325    0.139    0.451 

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: 2,163,617
Number of extensions: 87483
Number of successful extensions: 365
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 360
Number of HSP's successfully gapped: 1
Length of query: 727
Length of database: 1,619,870
Length adjustment: 92
Effective length of query: 635
Effective length of database: 1,184,250
Effective search space: 751998750
Effective search space used: 751998750
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: 134 (56.2 bits)