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= 0004.0077.p
         (387 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312358|ref|YP_003776450.1| hypothetical protein Hsero_3054...   635   0.0  
gi|300309967|ref|YP_003774059.1| permease [Herbaspirillum serope...    77   3e-15

>gi|300312358|ref|YP_003776450.1| hypothetical protein Hsero_3054
           [Herbaspirillum seropedicae SmR1]
          Length = 374

 Score =  635 bits (1639), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/387 (89%), Positives = 361/387 (93%), Gaps = 13/387 (3%)

Query: 1   MLGFDFRVARIVWTVFLVALLLYVTYTISATVLVLVFAVFFSYLVYPLVEQVERVRPAKV 60
           MLGFD RVARIVWTVFLVALLLYVTYTISATVLVLVFAVFFSYLVYPLVE +ERVRP +V
Sbjct: 1   MLGFDLRVARIVWTVFLVALLLYVTYTISATVLVLVFAVFFSYLVYPLVELIERVRPPRV 60

Query: 61  PRAVSIAVVFVLAIGIVAAVATIFGARIQEEALRLSEQLPALLRSNDAVSKIPLPGFAEP 120
           PR VSIA+VFVLAI IVA VATIFGARIQEEALRLSEQLPALLRSNDAVS++PLPGFAEP
Sbjct: 61  PRTVSIALVFVLAIAIVATVATIFGARIQEEALRLSEQLPALLRSNDAVSRLPLPGFAEP 120

Query: 121 LRARILGFIRDQLANGTDQAMPLAKQFGMGVMHAASNLIYLVLVPVISFLLIKEAPAMRD 180
           LRARILGF+RDQLA GTDQAMPLAKQFG+GVMHAASNLIYLVLVPVISFLLIKEAPAMR+
Sbjct: 121 LRARILGFVRDQLAAGTDQAMPLAKQFGVGVMHAASNLIYLVLVPVISFLLIKEAPAMRE 180

Query: 181 EILSWMNRSNRKLWDGIIKDLDVLLSRYVRALLFLSIATLVAYSIAFSLMGVPYAMLLAG 240
           E+LSWM+R+NRKLWDGI+ DLDVLLSRYVRALLFLS+AT VAYSIAFSLMGVPYAMLLAG
Sbjct: 181 EMLSWMSRANRKLWDGIVTDLDVLLSRYVRALLFLSVATFVAYSIAFSLMGVPYAMLLAG 240

Query: 241 LAAVLEFIPFAGPLAASAAALVVAGFSGYDHLLWLVGFIVAYRVFQDYVLNPYLMSEGVE 300
           LAAVLEFIPFAGPLAASAAALVVAGFS YDHLLWLVGFIVAYRVFQDYVLNPYLMSEGVE
Sbjct: 241 LAAVLEFIPFAGPLAASAAALVVAGFSAYDHLLWLVGFIVAYRVFQDYVLNPYLMSEGVE 300

Query: 301 VSPLMVILGLLAGDQLGGVAGIFLSVPVMAALKIIFTRASAAQKARRAAEAREAELAAQA 360
           VSPLMVILGLLAGDQLGGVAGIFLSVPVMAALKIIFTRASAAQKARRA+EAR+AEL   A
Sbjct: 301 VSPLMVILGLLAGDQLGGVAGIFLSVPVMAALKIIFTRASAAQKARRASEARQAEL---A 357

Query: 361 AQEALRSAEVAEPATAPPALPPTGRTS 387
           AQEALR        T PP  PPTG  S
Sbjct: 358 AQEALR--------TEPP--PPTGSAS 374


>gi|300309967|ref|YP_003774059.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 360

 Score = 76.6 bits (187), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 85/310 (27%), Positives = 147/310 (47%), Gaps = 24/310 (7%)

Query: 42  SYLVYPLVEQV--ERVRPAKVPRAVSIAVVFVLAIGIVAAVATIFGARIQEEALRLSEQL 99
            Y + P V+ +   R+ P +VPR V++ ++ +L I    A+  I    +  +   L  Q+
Sbjct: 43  GYALNPGVDWIASRRLGPVRVPRFVAVTIMVLLLILAGLALVLIVVPLVLRQIPLLQAQV 102

Query: 100 PALLRSNDAVSKIPLPGFAEPLR---ARILGFIRDQLANGTDQA----MPLAKQFGMGVM 152
           P LL   +A     L      +R   A I   +  Q++  +D+     +  AK  G  ++
Sbjct: 103 PPLLDKLNAFVSPRLHQLGIDVRLDLAGIKSLLTQQISTSSDEVWTSVLASAKVGGTALL 162

Query: 153 HAASNLIYLVLVPVISFLLIKEAPAM--RDEIL---SWMNRSNRKLWDGIIKDLDVLLSR 207
              +NL++   VP++ F L+++      R +IL    W  R N      +  ++D LL +
Sbjct: 163 TWLANLLF---VPMVLFYLLQDWHQFIKRMQILIPRRWAGRINT-----MAAEVDGLLGQ 214

Query: 208 YVRALLFLSIATLVAYSIAFSLMGVPYAMLLAGLAAVLEFIPFAGPLAASAAALVVA--G 265
           Y+R  L + +   V YS+A +  G   A+ +  L  +L FIP+ G       A++ A   
Sbjct: 215 YLRGQLLVMLVLAVYYSVALTAAGFDSALPVGVLTGLLVFIPYVGFGLGLVLAILAAILQ 274

Query: 266 FSGYDHLLWLVGFIVAYRVFQDYVLNPYLMSEGVEVSPLMVILGLLAGDQLGGVAGIFLS 325
           F G   LLW+       +V + ++L P L+ E + + PL+VI  LLA  QL G  G+ L+
Sbjct: 275 FDGAIGLLWVALIYGVGQVLESFILTPKLVGERIGLHPLVVIFALLAFGQLFGFVGVLLA 334

Query: 326 VPVMAALKII 335
           +P  A + +I
Sbjct: 335 LPASAIVSVI 344


  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
   0.327    0.139    0.397 

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: 942,103
Number of extensions: 35802
Number of successful extensions: 225
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 3
Length of query: 387
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 300
Effective length of database: 1,207,925
Effective search space: 362377500
Effective search space used: 362377500
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 (21.7 bits)
S2: 131 (55.1 bits)