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= 0001.4561.p
         (388 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313961|ref|YP_003778053.1| SMF protein involved in DNA upt...   473   e-135

>gi|300313961|ref|YP_003778053.1| SMF protein involved in DNA uptake
           protein [Herbaspirillum seropedicae SmR1]
          Length = 378

 Score =  473 bits (1218), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 269/363 (74%), Positives = 301/363 (82%), Gaps = 4/363 (1%)

Query: 25  AAWLRLSFTEGVGPSLARRLLSTFGLPECIWQADHAALSAVVPAQVATALLRAPSTVQRE 84
           A WLRLS  EGVGP+ ARRLL+ FGLP  +WQAD +AL+AVV   +A  LLRAP+   R 
Sbjct: 19  AWWLRLSLAEGVGPATARRLLAAFGLPGQLWQADASALAAVVSPALAARLLRAPTPAVRA 78

Query: 85  RIAATLAWVQRPGQTIVTLADAAYPQSLLNIADPPLLLYLRGHPALLAAPALAVVGSRNA 144
           +IAATLAW+Q+PG  I+TLAD+ YP +LL+IADPPLLLYLRG PA L A A+AVVGSRNA
Sbjct: 79  QIAATLAWLQQPGHAILTLADSRYPPALLDIADPPLLLYLRGDPAWLGAEAVAVVGSRNA 138

Query: 145 TTQGITHAARFSEELSRAGLTIVSGLALGIDTAAHEGGLRGSGSTVAVIGTGIDLDYPRR 204
           T QGI HA+RFS ELSRAGL+IVSGLALGID AAHEGGL G GSTVAVIGTGID+ YPRR
Sbjct: 139 TAQGIAHASRFSRELSRAGLSIVSGLALGIDAAAHEGGLDGPGSTVAVIGTGIDIVYPRR 198

Query: 205 NRALAQRIAEGGCIVSEYALGTPPLAANFPRRNRLISGLSRAVLVVEAAAQSGSLITARM 264
           + ALA RIA  GCIVSEY LGTPPLA+NFPRRNRLISGL+RAVLVVEAAAQSGSLITARM
Sbjct: 199 HEALAARIAAAGCIVSEYPLGTPPLASNFPRRNRLISGLARAVLVVEAAAQSGSLITARM 258

Query: 265 AAEQGRDVFAIPGSIHAPLSKGCHQLIRQGAKLVETTQDMLDELPGWSLPQAVPMTISSE 324
           AAEQGRDVFAIPGSIHAPL+KGCHQLIRQGAKLVETTQDMLDELP     QAV +   S 
Sbjct: 259 AAEQGRDVFAIPGSIHAPLAKGCHQLIRQGAKLVETTQDMLDELPS---RQAVRVAHPSP 315

Query: 325 RNADDNVDPTSRLVLQAMGHDPLDADTLAQRCKLDVAKLAGILLTLELQGLVELLPGARY 384
           ++  D+ D  + LV+QAM HDP+D DTLA RC L+ A LAG+LLTLEL G +ELLPGA Y
Sbjct: 316 QSQVDD-DAMTSLVMQAMAHDPVDIDTLAARCGLEAAVLAGLLLTLELAGRIELLPGALY 374

Query: 385 RRL 387
           RRL
Sbjct: 375 RRL 377


  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
   0.319    0.134    0.387 

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: 1,194,900
Number of extensions: 50810
Number of successful extensions: 207
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 1
Length of query: 388
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 301
Effective length of database: 1,207,925
Effective search space: 363585425
Effective search space used: 363585425
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 (21.8 bits)
S2: 131 (55.1 bits)