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= 0002.0121.p
         (247 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasm...   343   6e-96
gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasm...    59   4e-10

>gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 451

 Score =  343 bits (881), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 163/246 (66%), Positives = 197/246 (80%)

Query: 1   MALIGTMVNAHGGRWFDEKWQPQLDTPEWAQAVGLYVDLLRKYGPADAVQNGFNENLALF 60
           MA+I TM NA GGRWFDE+WQPQL +PEW ++V  YVDL+RKYGP  A  NGFNENL LF
Sbjct: 206 MAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAFYVDLMRKYGPPGASSNGFNENLVLF 265

Query: 61  AAGKCAMWIDATVAAGTLYHGKNSKVFDKTAFVAAPTATTAKGAQWLWVWALAVPHSSNS 120
           ++GKC MW+DATVAAG LYHGK+SKV DKTAF  +P   T KG+ WLW+W+LAVP SS S
Sbjct: 266 SSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPSPMQVTDKGSHWLWIWSLAVPKSSKS 325

Query: 121 KEAAKKFAVWATSKEYIRLVAEKDGWGLAPPGTRESTYASVGYLRASPYADFVLNAIRSA 180
           ++AAKKFA WATSKEYI LVA+  GW L PPGTR STYAS  Y + SP++DFVL+AI++A
Sbjct: 326 QDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRNSTYASAEYKKVSPFSDFVLDAIQTA 385

Query: 181 DPDSPTLKPVPYVGIQLVTIPEFPSIGTFTGQAIARALAGRSSVEAALKTSQTITMRLMQ 240
           D + PT+KPVPY G+Q  TIPEF SIGT TGQAIA ALAG+++ +AAL  +Q   +R+M+
Sbjct: 386 DANKPTVKPVPYTGVQFATIPEFQSIGTVTGQAIAGALAGKTTSDAALDAAQAQAVRMMR 445

Query: 241 QGRYIK 246
           QGRYIK
Sbjct: 446 QGRYIK 451


>gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 433

 Score = 58.9 bits (141), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 97/246 (39%), Gaps = 38/246 (15%)

Query: 10  AHGGRWFDEKWQPQLDTPEWAQAVGLYVDLLRKYGPADAVQNGFNENLALFAAGKCAMWI 69
           A GG+W D+  QP  ++P   +A  LY DL  KY P  A    ++  L  F +GK A  I
Sbjct: 213 AQGGQWTDKNNQPAFNSPAAVKATQLYADLF-KYAPPGAATYDWSNALEAFRSGKVAFMI 271

Query: 70  DATVAAGTLYHGKNSKVFDKTAFV--AAPTATTAKGAQWLWVWALAVPHSSNSKEAAKKF 127
           ++T  A  +     S V DK  +    AP  + A G   L + A+       +++AA KF
Sbjct: 272 ESTPFADWMEDSSKSSVADKVGYARPPAPLPSAAYG-HGLAISAVGAKDEC-TRQAAGKF 329

Query: 128 AVWATSKEYIRLVAEKDGWGLAPPGTRESTYASVGYLRASPYADFVLNAIRSADPDSPTL 187
             +AT KE                            LR   ++D+  ++   +D     +
Sbjct: 330 IAFATGKE-----------------------QEQARLREKVFSDYNRSSTIQSDYFQKNV 366

Query: 188 KPVPYVGIQLVT---------IPEFPSIGTFTGQAIARALAG-RSSVEAALKTSQTITMR 237
           KP    G++  T          P++P IG   G A+     G +  +  AL  +      
Sbjct: 367 KPQILAGLKDTTPVSKLTIWPSPQWPDIGDNLGVALEEVFTGTQKDITRALDEAAQYAQD 426

Query: 238 LMQQGR 243
            M+  R
Sbjct: 427 AMEHAR 432


  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
   0.318    0.131    0.407 

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: 792,519
Number of extensions: 31203
Number of successful extensions: 91
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 90
Number of HSP's successfully gapped: 2
Length of query: 247
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 164
Effective length of database: 1,226,865
Effective search space: 201205860
Effective search space used: 201205860
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: 129 (54.3 bits)