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= 0002.0111.p
         (444 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...   775   0.0  
gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasm...   112   8e-26

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

 Score =  775 bits (2002), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 380/431 (88%), Positives = 401/431 (93%)

Query: 14  AAAIAILGTAGLAFAEPVTLNIASINNPDMIELQKLSPQFEKANPDIKLRWVTMEESVLR 73
           AAAI+ L  AGLA AEPVTLNIASINNPDMIELQKL+P FEKANPDIKLRWVTMEESVLR
Sbjct: 21  AAAISTLFAAGLAQAEPVTLNIASINNPDMIELQKLAPAFEKANPDIKLRWVTMEESVLR 80

Query: 74  QRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLPADYDEADLIKTVREGLTSDG 133
           QRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLPADYDEADLIK VREGL+ DG
Sbjct: 81  QRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLPADYDEADLIKPVREGLSVDG 140

Query: 134 KLYALPFYAESSMTYYRKDLFAQKNLKMPEKPTWEEIGKLAAQLHDPAKGVYGICLRGRA 193
           KLYALPFYAESSMTYYRKDLF QK L MP++PTW+EI KLAAQLHDPAKGVYGICLRGRA
Sbjct: 141 KLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKLAAQLHDPAKGVYGICLRGRA 200

Query: 194 GWGENMALVGTMVNAYGGRWFDEKWQPQLDTPEWKQAVNFYVDLMRKSGPPGASSNGFNE 253
           GWGENMA++ TM NA+GGRWFDE+WQPQL +PEWK++V FYVDLMRK GPPGASSNGFNE
Sbjct: 201 GWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAFYVDLMRKYGPPGASSNGFNE 260

Query: 254 NLVLFSGGKCGMWVDATVAAGMLYHGKDSKVSDKVAFAPAPMATTDKGSHWLWIWSLAVP 313
           NLVLFS GKCGMWVDATVAAGMLYHGKDSKV+DK AFAP+PM  TDKGSHWLWIWSLAVP
Sbjct: 261 NLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPSPMQVTDKGSHWLWIWSLAVP 320

Query: 314 KSSKSQDAARKFAAWATSKDYIKLVAKDSGWALVPPGTRTSTYASAEYKKASPFSDFVLD 373
           KSSKSQDAA+KFAAWATSK+YI LVAKDSGWALVPPGTR STYASAEYKK SPFSDFVLD
Sbjct: 321 KSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRNSTYASAEYKKVSPFSDFVLD 380

Query: 374 AIQKADANNPTVKPVPYTGIQFATIPEFQSIGTITGQAIAGALAGKGPADAALKTAQAQT 433
           AIQ ADAN PTVKPVPYTG+QFATIPEFQSIGT+TGQAIAGALAGK  +DAAL  AQAQ 
Sbjct: 381 AIQTADANKPTVKPVPYTGVQFATIPEFQSIGTVTGQAIAGALAGKTTSDAALDAAQAQA 440

Query: 434 VRMMKQGRYIK 444
           VRMM+QGRYIK
Sbjct: 441 VRMMRQGRYIK 451


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

 Score =  112 bits (279), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 100/333 (30%), Positives = 151/333 (45%), Gaps = 23/333 (6%)

Query: 13  LAAAIAILGTAGLAFAEPVTLNIASINNPDMIELQKLS---PQFEKANPDIKLRWVT--- 66
           L AA A+LG A      P+  +  S N P +  L + S      EK+  D + R  T   
Sbjct: 16  LGAACAVLGAA-----LPLVASAQSCNVPVLKVLAQKSLGLTVMEKSLADYQKRSGTRIE 70

Query: 67  ---MEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTG-LPADYDEADLI 122
                E+  R +   D AT +G + +  +       +A  GW+ P+    P D D  D +
Sbjct: 71  ISYFGENDRRAKSRLDAATKAGSYQVYYVDEANVAEFASAGWIVPLLKYFPKDADYDDFL 130

Query: 123 KTVREGLTSDGKLYALPFYAESSMTYYRKDLFAQKNLKMPEKPTWEEIGKLAAQLHDPAK 182
              R   +     Y  P    S   +YR+DL  +  L +P   T +E+     +LH P  
Sbjct: 131 PGRRAVASYKDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPR--TLDELVADIKKLHSPP- 187

Query: 183 GVYGICLRGRAGWGENMALVGTMVNAYGGRWFDEKWQPQLDTPEWKQAVNFYVDLMRKSG 242
            VYG   RG+ G G N+      + A GG+W D+  QP  ++P   +A   Y DL  K  
Sbjct: 188 SVYGWVARGQRGSGMNVWRWAPFMLAQGGQWTDKNNQPAFNSPAAVKATQLYADLF-KYA 246

Query: 243 PPGASSNGFNENLVLFSGGKCGMWVDATVAAGMLYHGKDSKVSDKVAFA--PAPMATTDK 300
           PPGA++  ++  L  F  GK    +++T  A  +     S V+DKV +A  PAP+ +   
Sbjct: 247 PPGAATYDWSNALEAFRSGKVAFMIESTPFADWMEDSSKSSVADKVGYARPPAPLPSAAY 306

Query: 301 GSHWLWIWSLAVPKSSKSQDAARKFAAWATSKD 333
           G H L I ++   K   ++ AA KF A+AT K+
Sbjct: 307 G-HGLAISAVGA-KDECTRQAAGKFIAFATGKE 337


  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
   0.316    0.131    0.401 

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: 1,393,449
Number of extensions: 59970
Number of successful extensions: 179
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 2
Length of query: 444
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 356
Effective length of database: 1,203,190
Effective search space: 428335640
Effective search space used: 428335640
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 (21.6 bits)
S2: 132 (55.5 bits)