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= 0003.0082.p
         (347 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310369|ref|YP_003774461.1| sugar ABC transporter permease ...   451   e-128
gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto...   159   3e-40
gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ...   129   4e-31
gi|300311740|ref|YP_003775832.1| sugar ABC transporter permease ...   120   1e-28
gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ...   115   6e-27

>gi|300310369|ref|YP_003774461.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score =  451 bits (1160), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 264/333 (79%), Positives = 291/333 (87%), Gaps = 6/333 (1%)

Query: 15  PYFTSLVTVALLVVLFAMGSVAYDGFFSVQVVLNLLIDNAFLLVIGIGMTFVILSGGIDL 74
           P+FTS+VTV LLVV+   G++ YDGF S QV+LNLLIDNAFLLV+ IGMTFVILSGGIDL
Sbjct: 14  PWFTSMVTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAIGMTFVILSGGIDL 73

Query: 75  SVGSVLALTTMISAYMLQSWHWHPLLVIVCVLALGGLFGAAMGVLIHFFKLQPFIVTLAG 134
           SVGSVLALTTM++A++LQ+WHWHPLLVIV VL +G  FGAAMG +IH+FKLQ FIVTLAG
Sbjct: 74  SVGSVLALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIHYFKLQAFIVTLAG 133

Query: 135 MFLARGLCYLISINSITIDDPLFVAMSQTRLEFGLGDAFVSPSVVIAVLMLALAIYLAHY 194
           MFLARGLCYLISINSITIDDPLF  +SQTRLE  L   F+SPSVVIA+ MLALAI++AH 
Sbjct: 134 MFLARGLCYLISINSITIDDPLFTTLSQTRLE--LAGLFISPSVVIALFMLALAIWMAHC 191

Query: 195 TRFGRAVYAVGGNEQSALLMGLPVGRTKVAIYAFSGFCAALAGVLFSFYMLSGYGLHAQG 254
           TRFGRAVYA+GGNE SALLMGLPVGRTKV +YAFSG CAA+AGVLFSFYMLSGYGLHAQG
Sbjct: 192 TRFGRAVYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFYMLSGYGLHAQG 251

Query: 255 TELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIVIGVLLF 314
            ELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKI IG LLF
Sbjct: 252 VELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIFIGALLF 311

Query: 315 VFCLAQRLMSLGAAKAADANAGGGSVKPAAQAA 347
           VFC+AQR++SLGA +   A    GS K A   A
Sbjct: 312 VFCVAQRVISLGALRGKPA----GSAKAAPAGA 340


>gi|300310397|ref|YP_003774489.1|
           ribose/xylose/arabinose/galactoside ABC transporter
           permease [Herbaspirillum seropedicae SmR1]
          Length = 328

 Score =  159 bits (402), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 118/314 (37%), Positives = 180/314 (57%), Gaps = 15/314 (4%)

Query: 3   NFRSLFHQLLATPYFTSLVTVALLVVLFAMGSVAYDGFFSVQVVLNLLIDNAFLLVIGIG 62
            +RSL H  LA P    LV V+LL+       +A D FF++    N+L   + + ++ +G
Sbjct: 20  RWRSLIHSPLALP-LAGLVVVSLLM------GLASDNFFTLSNWFNVLRQVSIVGILAVG 72

Query: 63  MTFVILSGGIDLSVGSVLALTTMISAYMLQSWHWHPLLVIVCVLALGGLFGAAMGVLIHF 122
           M+FVIL+GGIDLSVG+ +AL   ISA ++ +      L ++C + L    G   G L+ +
Sbjct: 73  MSFVILTGGIDLSVGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAW 132

Query: 123 FKLQPFIVTLAGMFLARGLCYLISINSITIDDPLFVAMSQTRLEFGLGDAFVSPSVVIAV 182
            ++   IVTLA M +ARG+  + S        P +++       FG+G   + P  VI +
Sbjct: 133 GRMPAIIVTLATMGVARGVGLIYSGGYPISGLPGWISW------FGVGRIGMVPVPVILM 186

Query: 183 LML-ALAIYLAHYTRFGRAVYAVGGNEQSALLMGLPVGRTKVAIYAFSGFCAALAGVLFS 241
           L++ ALA  L   T FGR VYA+GGNE +A L G+   R K+A+YA SGF + LA ++ +
Sbjct: 187 LIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILT 246

Query: 242 FYMLSGYGLHAQGTELDAIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLS 301
             ++SG      G ELDAIAAVV+GGT + GG G V GTL G ++LG++   +   G ++
Sbjct: 247 GRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMG-IN 305

Query: 302 SWWTKIVIGVLLFV 315
            +   I+ GV++ +
Sbjct: 306 PYLQDIIRGVIILL 319


>gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 344

 Score =  129 bits (323), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 102/294 (34%), Positives = 158/294 (53%), Gaps = 11/294 (3%)

Query: 40  FFSVQVVLNLLIDNAFLLVIGIGMTFVILSGGIDLSVGSVLALTTMISAYMLQSWHWHPL 99
           F S +  +N+L   A  LV+  GMTFVIL+ GIDLSVGSVLA++ ++   M  S    P 
Sbjct: 60  FASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLG--MQVSLGAAPG 117

Query: 100 LVIVCVLALGGLFGAAMGVLIHFFKLQPFIVTLAGMFLARGLCYLISINSITIDDPLFVA 159
             I   +  G + G   G ++    +  F+VTL  M   RG  YL++  +  +++ +   
Sbjct: 118 WAIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDI--- 174

Query: 160 MSQTRLEF-GLGDAFVSPSVV-IAVLMLALAIYLAHYTRFGRAVYAVGGNEQSALLMGLP 217
                 E+ G GD    P ++ +AV ++ L+  +   T  G  +YA+GGN Q+A L G+ 
Sbjct: 175 ---PSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIR 231

Query: 218 VGRTKVAIYAFSGFCAALAGVLFSFYMLSGYGLHAQGTELDAIAAVVIGGTLLTGGYGYV 277
           VG   + +Y+ SG  + LAG + +  +    G    G ELDAIAAVV+GGT L GG G +
Sbjct: 232 VGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSI 291

Query: 278 AGTLTGVLILGVIQTLIAFDGTLSSWWTKIVIGVLLFVFCLAQRLMSLGAAKAA 331
            GT+ G LI+GV+   +   G LSS+W  +  G ++ +  +  +     AA++A
Sbjct: 292 WGTVVGALIIGVMNNGLTILG-LSSFWQYVAKGAVIVLAVILDKWRQKDAAQSA 344


>gi|300311740|ref|YP_003775832.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 379

 Score =  120 bits (302), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 113/341 (33%), Positives = 167/341 (48%), Gaps = 33/341 (9%)

Query: 5   RSLFHQLLATPYFTSLVTVALLVVLFAMGSVAYDGFFSVQVVLNLLIDNAFLLVIGIGMT 64
            +L  +LL  P F SL  V L+ ++F + +    G F++  V+N +   A+L +I +   
Sbjct: 26  ENLVSRLLGRPEFASLAGVILVFLVFGL-TAGDSGMFNLDGVVNWMQVAAYLGIIAVAAC 84

Query: 65  FVILSGGIDLSVGSVLALTTMISAYMLQSWHWHPLLVIVCVLALGGLFGAAMGVLIHFFK 124
            +++ G  DLS+GS++ L  M+ A     + W   L ++   A     G   G L+   +
Sbjct: 85  LLMIGGEFDLSIGSMIGLAGMMVAIPTVYFGWPFWLAVLFAFAASMGLGWLNGYLVMKTR 144

Query: 125 LQPFIVTLAGMFLARGLCYLISI---NSITID--------DPLFVAMSQTRLEFGL---- 169
           L  FIVTLA +F+ RGL   +SI   N   +         D L   +    +  GL    
Sbjct: 145 LPSFIVTLAFLFILRGLTLALSILFANRTIVSGVGERAAHDWLGQLLFSGNVGAGLFSWL 204

Query: 170 -----------GDAFVS--PSVVI--AVLMLALAIYLAHYTRFGRAVYAVGGNEQSALLM 214
                      G   V+  P V++  AV+ LA +  LA  TR G  ++AVGG+  +A  M
Sbjct: 205 ARHGWIATVADGTPLVTGIPKVILWWAVVALAASFVLAR-TRLGNWIFAVGGDAVAAKNM 263

Query: 215 GLPVGRTKVAIYAFSGFCAALAGVLFSFYMLSGYGLHAQGTELDAIAAVVIGGTLLTGGY 274
           G+PV + K+ ++ F+ FCA L  VL      S         E +AI A VIGG LLTGGY
Sbjct: 264 GVPVRKVKIGLFVFTAFCACLFAVLQVGDFGSAAADRGLQKEFEAIIAAVIGGALLTGGY 323

Query: 275 GYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIVIGVLLFV 315
           G V G   G LI GV+Q  I +   LSS W ++ +GV+L V
Sbjct: 324 GSVIGACFGALIFGVVQIGITYT-NLSSDWFRVFLGVMLLV 363


>gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 347

 Score =  115 bits (288), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 108/295 (36%), Positives = 160/295 (54%), Gaps = 12/295 (4%)

Query: 25  LLVVLFAMGSVAYDGFFSVQVVLNLLIDNAFLLVIGIGMTFVILSGGIDLSVGSVLALTT 84
           LL++LF   S A   F  V  ++++L   A   V+ I  T+VI++ GIDLSVG+++    
Sbjct: 44  LLMILFF--SFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCA 101

Query: 85  MISAYMLQSWHWHPLLVIVCVLALGGLFGAAMGVLIHFFKLQPFIVTLAGMFLARGLCYL 144
           +++  +L +W     L I   +  G L G   G++I   K+ PFI TL  M L +GL  +
Sbjct: 102 VMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLV 161

Query: 145 IS-INSITIDDPL-FVAMSQTRLEFGLGDAFVSPSVVIAVLMLAL----AIYLAHYTRFG 198
           IS    I  +D   F A++Q  L   +GD   S  +  AVL+L L    A  + + T FG
Sbjct: 162 ISGTRPIYFNDTEGFSAIAQDSL---IGDLIPSLPIPNAVLILFLVAIGASIILNKTVFG 218

Query: 199 RAVYAVGGNEQSALLMGLPVGRTKVAIYAFSGFCAALAGVLFSFYMLSGYGLHAQGTELD 258
           R  +A+G NE++  L G+ V   KVA+Y FSG    +AG++ +  + S      QG ELD
Sbjct: 219 RYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELD 278

Query: 259 AIAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIVIGVLL 313
           AIAAVVIGGT L+GG G + GT+ G  I+ V+   +        W T +V GV++
Sbjct: 279 AIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQT-VVTGVII 332


  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
   0.330    0.143    0.426 

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: 838,558
Number of extensions: 29619
Number of successful extensions: 251
Number of sequences better than 1.0e-08: 21
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 24
Length of query: 347
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 261
Effective length of database: 1,212,660
Effective search space: 316504260
Effective search space used: 316504260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 131 (55.1 bits)