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= 0002.0013.p
         (152 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314071|ref|YP_003778163.1| amino acid ABC transporter peri...   238   1e-64
gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC t...   190   5e-50
gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC t...   187   3e-49
gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC t...   125   1e-30

>gi|300314071|ref|YP_003778163.1| amino acid ABC transporter
           periplasmic protein [Herbaspirillum seropedicae SmR1]
          Length = 402

 Score =  238 bits (608), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 119/159 (74%), Positives = 128/159 (80%), Gaps = 10/159 (6%)

Query: 4   FGIPLQALLSQLL--------LGLVN--GSFYADSWYWDTNEETRKFAKRYFEKQKKMPS 53
           FGI   A L+ LL        L L N  G +  DSWYWD NEETR FAKRYF  +KKMPS
Sbjct: 244 FGITKTAKLAGLLVFINDVHSLTLKNTEGLYLTDSWYWDANEETRAFAKRYFAVRKKMPS 303

Query: 54  SLQAADYSAALQYLQAVKAAGTDDSDKVMAQLRKTKFNDVFQKNGYLRADGRVVHDMYLY 113
           SLQAADYSAALQYL+ VK  GTDDSDKVMA LRK KFND++QKNGYLRADGRV+HDMYLY
Sbjct: 304 SLQAADYSAALQYLKVVKEIGTDDSDKVMAALRKAKFNDMYQKNGYLRADGRVMHDMYLY 363

Query: 114 QVKTPAESKYPWDYYKLVQTIPAEQAWTTKAESKCSAWK 152
           QVK  +ESKYPWDYYKLVQTIPAEQAWTTKAESKC+AWK
Sbjct: 364 QVKAQSESKYPWDYYKLVQTIPAEQAWTTKAESKCAAWK 402


>gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 404

 Score =  190 bits (482), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 88/138 (63%), Positives = 102/138 (73%)

Query: 15  LLLGLVNGSFYADSWYWDTNEETRKFAKRYFEKQKKMPSSLQAADYSAALQYLQAVKAAG 74
           L L L  G +  D WYWD N++TR +A RYF K KKMPS  QA D SA  QYL+AVKA G
Sbjct: 267 LGLSLTQGMYLTDGWYWDLNDQTRAWANRYFMKMKKMPSMFQAGDASAVGQYLKAVKAVG 326

Query: 75  TDDSDKVMAQLRKTKFNDVFQKNGYLRADGRVVHDMYLYQVKTPAESKYPWDYYKLVQTI 134
           + D+DKVM  LRK + ND F  NG +R DGR+VHDMYL +VK P+ESK PWDYYKLVQTI
Sbjct: 327 STDADKVMDYLRKNRINDFFTSNGVVRPDGRMVHDMYLMEVKKPSESKRPWDYYKLVQTI 386

Query: 135 PAEQAWTTKAESKCSAWK 152
           P EQA+ TKAESKC+ WK
Sbjct: 387 PGEQAYMTKAESKCALWK 404


>gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 404

 Score =  187 bits (475), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/154 (60%), Positives = 116/154 (75%), Gaps = 4/154 (2%)

Query: 1   MELFGIPLQALLSQLLLGLVN--GSFYADSWYWDTNEETRKFAKRYFEKQKKMPSSLQAA 58
           M+L G+ L  +     LGL N  G    DSWYWD +E +RKFA+R+F+K KKMPS+ QAA
Sbjct: 252 MKLVGL-LMVINDIHALGLANAEGLMMTDSWYWDKDEPSRKFAERFFQKMKKMPSTHQAA 310

Query: 59  DYSAALQYLQAVKAAGTDDSDKVMAQLRKTKFNDVFQKNGYLRADGRVVHDMYLYQVKTP 118
            YSA   YL+AV+A GTDDS KVMAQL+KT+ +D + K G +RADGR +HDMYLYQVK+P
Sbjct: 311 AYSATTTYLKAVQAIGTDDSTKVMAQLKKTRIDDFYNK-GSIRADGRNIHDMYLYQVKSP 369

Query: 119 AESKYPWDYYKLVQTIPAEQAWTTKAESKCSAWK 152
           AESK PWDY KL++TIP EQA+T+ A+SKCS  K
Sbjct: 370 AESKKPWDYLKLLETIPGEQAFTSVADSKCSLLK 403


>gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 410

 Score =  125 bits (314), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/139 (47%), Positives = 89/139 (64%), Gaps = 4/139 (2%)

Query: 6   IPLQALLSQL-LLGL--VNGSFYADSWYWDTNEETRKFAKRYFEKQKKM-PSSLQAADYS 61
           + L   LS +  LGL    G  Y D +YWD +E+TR F+KR+  + K + P+ +QA  YS
Sbjct: 260 VALLVFLSDVHALGLEAAQGLVYTDGFYWDYDEQTRAFSKRFESQFKNIKPTMVQAGVYS 319

Query: 62  AALQYLQAVKAAGTDDSDKVMAQLRKTKFNDVFQKNGYLRADGRVVHDMYLYQVKTPAES 121
           +  Q+L+A  AA T D   V  ++R+    D   +N  +R DGRV+HDMYLYQVKTPAES
Sbjct: 320 SVYQFLKARAAAKTSDWKVVAQKMREIPIADAVMRNASIRPDGRVIHDMYLYQVKTPAES 379

Query: 122 KYPWDYYKLVQTIPAEQAW 140
           K PWDY KL+  IPA+QA+
Sbjct: 380 KGPWDYLKLLSVIPAQQAF 398


  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
   0.317    0.129    0.392 

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: 401,074
Number of extensions: 13378
Number of successful extensions: 61
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 59
Number of HSP's successfully gapped: 5
Length of query: 152
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 75
Effective length of database: 1,255,275
Effective search space: 94145625
Effective search space used: 94145625
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: 126 (53.1 bits)