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= 0001.0692.p
         (336 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310064|ref|YP_003774156.1| sugar ABC transporter permease ...   578   e-166
gi|300310397|ref|YP_003774489.1| ribose/xylose/arabinose/galacto...   200   2e-52
gi|300310383|ref|YP_003774475.1| sugar ABC transporter permease ...   160   1e-40
gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease ...   157   2e-39
gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease ...   154   1e-38

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

 Score =  578 bits (1490), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 311/335 (92%), Positives = 319/335 (95%)

Query: 2   HKNDTGAAVAARSSSSVSQWLLHRLGMLPVLVVLYLLFYALTIYLSGDGGSNFATTENTM 61
           H +D     A RSSS+ +QWLLHRLGMLPVLVVLYLLFY LT+YLSGDG SNFA+ ENTM
Sbjct: 8   HTHDAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTM 67

Query: 62  NILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLSAAPGWSIPMFIVSG 121
           NILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSL AAPGW+IPMFI SG
Sbjct: 68  NILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFSG 127

Query: 122 LVMGMVNGAMVAFLNINAFVVTLGTMTAFRGAAYLLADGTTVLNSDIPSFEWIGNGDFLR 181
           LVMGMVNGAMVA LNINAFVVTLGTMTAFRGAAYLLADGTTVLN+DIPSFEWIGNGDFL 
Sbjct: 128 LVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDFLH 187

Query: 182 VPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFS 241
           VPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFS
Sbjct: 188 VPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFS 247

Query: 242 GLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGTIWGTVVGALIIGVMNNG 301
           GLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVG+IWGTVVGALIIGVMNNG
Sbjct: 248 GLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNG 307

Query: 302 LTILGLSSFWQYVAKGAVIVLAVILDKWRQKDATQ 336
           LTILGLSSFWQYVAKGAVIVLAVILDKWRQKDA Q
Sbjct: 308 LTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAAQ 342


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

 Score =  200 bits (508), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 133/340 (39%), Positives = 204/340 (60%), Gaps = 22/340 (6%)

Query: 1   MHKNDTGAAVAARSSSSVSQW--LLHRLGMLPV--LVVLYLLFYALTIYLSGDGGSNFAT 56
           M  +      A+  +++ ++W  L+H    LP+  LVV+ LL         G    NF T
Sbjct: 1   MPHDANALPAASLHTAASARWRSLIHSPLALPLAGLVVVSLLM--------GLASDNFFT 52

Query: 57  TENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLSAAPGWSIPM 116
             N  N+LRQV+I  +LA GM+FVILT GIDLSVG+ +A++  +     L    G   P+
Sbjct: 53  LSNWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGAAMALAGTI--SAGLIVNSGLPAPL 110

Query: 117 FIVSGL----VMGMVNGAMVAFLNINAFVVTLGTMTAFRGAAYLLADGTTVLNSDIPS-F 171
            ++ G+     +G++NGA+VA+  + A +VTL TM   RG   + + G  +  S +P   
Sbjct: 111 ALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATMGVARGVGLIYSGGYPI--SGLPGWI 168

Query: 172 EWIGNGDFLRVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLL 231
            W G G    VP  + + + V  L+W++L++T  G H+YAIGGN  AARL+G++   + L
Sbjct: 169 SWFGVGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTTRIKL 228

Query: 232 FVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGTIWGTVVG 291
            VY+ISG  SGLA  +   RL     N G G+ELDAIAAVVLGGT++ GG G + GT++G
Sbjct: 229 AVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVGTLIG 288

Query: 292 ALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAV-ILDKWR 330
           A+++G++NNGL ++G++ + Q + +G +I+LA+ I  +WR
Sbjct: 289 AVLLGILNNGLNLMGINPYLQDIIRGVIILLAIYIAREWR 328


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

 Score =  160 bits (406), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 119/315 (37%), Positives = 180/315 (57%), Gaps = 28/315 (8%)

Query: 33  VVLYLLFYALTIYLSGDGGSNFATTENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGS 92
           ++L +LF++           NF   +N ++IL+  A+N VLA   T+VI+T+GIDLSVG+
Sbjct: 43  LLLMILFFSF-------ASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGT 95

Query: 93  VLAVSAVL--------GMQVSLSAAPGWSIPMFIVSGLVMGMVNGAMVAFLNINAFVVTL 144
           ++   AV+        GM + L  A        I  G + G ++G ++A L +  F+ TL
Sbjct: 96  MMTFCAVMAGVVLTNWGMPLPLGIAAA------IFFGALSGWISGMVIAKLKVPPFIATL 149

Query: 145 GTMTAFRGAAYLLADGTTVLNSDIPSFEWIGN----GDF---LRVPWLIWVAVAVVLLSW 197
           G M   +G + +++    +  +D   F  I      GD    L +P  + +   V + + 
Sbjct: 150 GMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGAS 209

Query: 198 VILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANG 257
           +IL KTV G + +A+G N +A RL+G++V    + VY+ SG   G+AG + ASRL  A  
Sbjct: 210 IILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQP 269

Query: 258 NWGSGYELDAIAAVVLGGTSLMGGVGTIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKG 317
             G GYELDAIAAVV+GGTSL GG GTI GT++GA I+ V+ NGL I+ ++  WQ V  G
Sbjct: 270 ALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTG 329

Query: 318 AVIVLAVILDKWRQK 332
            +I+LAV LD  R++
Sbjct: 330 VIIILAVYLDILRRR 344


>gi|300313727|ref|YP_003777819.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 352

 Score =  157 bits (396), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 109/295 (36%), Positives = 166/295 (56%), Gaps = 19/295 (6%)

Query: 54  FATTENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLG--MQVSLSAAP- 110
           F + ++  N+L   AI ++LA     VILT GIDLSV S LA+S ++   + +   A P 
Sbjct: 49  FLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNLALSGMMSALLAMHFPALPV 108

Query: 111 GWSIPMFIVSGLVMGMVNGAMVAFLNINAFVVTLGTMTAFRGAAYLLADGTTVLNSDIPS 170
           G  I M ++ GL++G++NG ++ +L +   VVTLG+M+ +RG  ++L+ G  V + ++P+
Sbjct: 109 GVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYRGMVFVLSGGAWVSSRNMPA 168

Query: 171 FEWIGNGDFLRVP--------WLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLT 222
                  DF+  P         L+W+    V+  W + R T  G  +YAIG +  AA   
Sbjct: 169 -------DFIAFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLYAIGNDPAAAAYV 221

Query: 223 GIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGV 282
           GI     LL+ Y +SG  +GLAG +  +R   A      G+EL  IAA V+GG S+ GGV
Sbjct: 222 GIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAACVIGGVSIAGGV 281

Query: 283 GTIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILD-KWRQKDATQ 336
           G + G V+GAL + V+NN L I+ +S FWQ    G VI+ AV+L+ + +Q    Q
Sbjct: 282 GQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILCAVVLNARGKQGRRKQ 336


>gi|300311610|ref|YP_003775702.1| sugar ABC transporter permease
           [Herbaspirillum seropedicae SmR1]
          Length = 328

 Score =  154 bits (388), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 111/321 (34%), Positives = 179/321 (55%), Gaps = 36/321 (11%)

Query: 26  LGMLPVLVVLYLLFYALTIYLSGDGGSNFATTENTMNILRQVAINLVLAAGMTFVILTAG 85
           LG++  L+ + ++F  L+         NF +    + +   +   +V++ GMTF+++  G
Sbjct: 24  LGLMAALLAMCVMFAFLS--------ENFLSAATFITLSNDIPPLVVMSVGMTFILIIGG 75

Query: 86  IDLSVGSVLAVSAVLGMQVSLSAAP---GWSI----PMFIVSGLVMGMVNGAMVAFLNIN 138
           IDLSVGSV+A++A +     LS A    GW +    P+ +V   + G + G +     I 
Sbjct: 76  IDLSVGSVMALAASM-----LSMAMVRWGWPLYAAAPLGVVVAALCGTLTGMVSVHWRIP 130

Query: 139 AFVVTLGTMTAFRGAAYLLADGTTVLNSDIPSFEWIGNG-DFLRVPWLIWV------AVA 191
           +F+V+LG +   RG AY + +  T         E+IG+  D +  P L  +      A+A
Sbjct: 131 SFIVSLGVLEIARGLAYQVTNSRT---------EYIGSAVDVISSPILFGMSPAFLSAIA 181

Query: 192 VVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASR 251
           +V+++ ++L +TVLG +   IG N +A RL+G+      +  +++ G  +G+A     SR
Sbjct: 182 IVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAALFQVSR 241

Query: 252 LYGANGNWGSGYELDAIAAVVLGGTSLMGGVGTIWGTVVGALIIGVMNNGLTILGLSSFW 311
           L  A+ N G G EL  IAAVV+GGTSLMGG G+I  T +G LII V+  GL  +G+S   
Sbjct: 242 LEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVGVSEPM 301

Query: 312 QYVAKGAVIVLAVILDKWRQK 332
           + +  GAVIV+AVILD +R++
Sbjct: 302 KRIITGAVIVVAVILDTYRRR 322


  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
   0.324    0.138    0.414 

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: 816,615
Number of extensions: 28720
Number of successful extensions: 259
Number of sequences better than 1.0e-08: 18
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 20
Length of query: 336
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 250
Effective length of database: 1,212,660
Effective search space: 303165000
Effective search space used: 303165000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 131 (55.1 bits)