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= 0038.0007.p
         (338 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter peripl...   620   e-179
gi|300310370|ref|YP_003774462.1| sugar ABC transporter periplasm...   167   2e-42

>gi|300313776|ref|YP_003777868.1| D-xylose ABC transporter
           periplasmic protein [Herbaspirillum seropedicae SmR1]
          Length = 338

 Score =  620 bits (1599), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 304/338 (89%), Positives = 322/338 (95%)

Query: 1   MNAILKKSVLALMAATTMSLVAGGAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL 60
           M A+LKK+VLALM  TT+S+VAG AMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL
Sbjct: 1   MKAMLKKTVLALMTVTTLSMVAGSAMADAKNPKIGFSIDDLRVERWARDRDFFTAAAEKL 60

Query: 61  GAKVFVQSADASEARQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120
           GAKV+VQSADASE RQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR
Sbjct: 61  GAKVYVQSADASEQRQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDR 120

Query: 121 LILNADVDAYISFDNEKVGEMQAEGVVKAQSKGNFYLLGGSPTDNNAKMLREGQMKVLKP 180
           LILNADVDAYISFDNEKVGEMQAEG++K ++KGNF+LLGGSPTDNNAKM REGQMK LKP
Sbjct: 121 LILNADVDAYISFDNEKVGEMQAEGILKVKNKGNFFLLGGSPTDNNAKMFREGQMKALKP 180

Query: 181 LIDKGDIKIVGQQWVKDWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK 240
            IDKGDIKIVGQQWVK+WNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK
Sbjct: 181 YIDKGDIKIVGQQWVKEWNPTEALSIVENALTANNNKIDAIVASNDGTAGGAIQALAAQK 240

Query: 241 LAGKVPVSGQDADLAAIKRVVAGTQTMTVYKPLKLIATEAANLSVHLARNEKPSYNSQYD 300
           LAGKVPVSGQDADLAA+KRVVAGTQTMTVYKPLK IATEAA LSV LARNEKP+YN+QYD
Sbjct: 241 LAGKVPVSGQDADLAAVKRVVAGTQTMTVYKPLKQIATEAAKLSVELARNEKPTYNAQYD 300

Query: 301 NGFKKVDTVLLKPIPLTKANVNILVDDGFYTQAQIGGK 338
           NGFKKVD++LLKPI LTK NV +LVDDGFYTQAQI G+
Sbjct: 301 NGFKKVDSLLLKPILLTKENVKVLVDDGFYTQAQIDGR 338


>gi|300310370|ref|YP_003774462.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 357

 Score =  167 bits (422), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 117/355 (32%), Positives = 198/355 (55%), Gaps = 28/355 (7%)

Query: 7   KSVLALMA-ATTMSLVAGGAMADAKNPK-IGFSIDDLRVERWARDRDFFTAAAEKLGAKV 64
           KSVL+ +A    ++L++  A   A++ + +G ++      RW  D +      ++ G + 
Sbjct: 4   KSVLSGIALGLGVTLMSISAQVSAQSKQLVGVAMPTKSSARWIADGNNMVKVLKEKGYQT 63

Query: 65  FVQSADASEARQISQIENLISRGVDVIVIVPFNATVLTNTIKEAKKAGIKVLSYDRLILN 124
            +Q A+     Q+SQIEN++++G  V+VI   + T LT+ +++A   G+KV++YDRLI  
Sbjct: 64  DLQYAEDDIPNQLSQIENMLTKGAKVLVIAAIDGTTLTDVLQKAADKGVKVIAYDRLIRG 123

Query: 125 A-DVDAYISFDNEKVGEMQAEGVVKA----QSKG--NFYLLGGSPTDNNAKMLREGQMKV 177
           + +VD Y +FDN +VG +QA+ + KA    + KG  N  L GGS  DNNA     G M V
Sbjct: 124 SKNVDYYATFDNFQVGVLQAQSLEKALGLKEGKGPFNIELFGGSSDDNNAFFFYNGAMSV 183

Query: 178 LKPLIDKGDIKIVGQQWVKD------WNPTEALSIVENALTA--NNNKIDAIVASNDGTA 229
           LKP ID G + +  +Q   D      W+P  A + ++N L+A   N K++A+++  DG +
Sbjct: 184 LKPYIDSGKLVVRSKQMGMDKVATLRWDPATAQARMDNLLSAYYTNAKVNAVLSPYDGLS 243

Query: 230 GGAIQALAAQKLAGKVP------VSGQDADLAAIKRVVAGTQTMTVYKPLKLIATEAANL 283
            G + +L  + +    P      VSGQDA++ ++K ++ G Q  T++K  + +A     +
Sbjct: 244 IGILSSL--RGVGYGTPQQPFPYVSGQDAEVPSVKSIIRGEQYSTIFKDTRELAKVTVGM 301

Query: 284 SVHLARNEKPSYN--SQYDNGFKKVDTVLLKPIPLTKANV-NILVDDGFYTQAQI 335
              +   ++P  N    Y+NG K V + LLKP+ + K+N   +LV  G+YT+AQ+
Sbjct: 302 VDAVLGGKQPQINDTKTYNNGVKVVPSYLLKPVVVDKSNWKEVLVGSGYYTEAQL 356


  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
   0.315    0.131    0.358 

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: 956,218
Number of extensions: 37600
Number of successful extensions: 141
Number of sequences better than 1.0e-08: 7
Number of HSP's gapped: 134
Number of HSP's successfully gapped: 7
Length of query: 338
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 252
Effective length of database: 1,212,660
Effective search space: 305590320
Effective search space used: 305590320
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: 42 (22.0 bits)
S2: 131 (55.1 bits)