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= 0001.3108.p
         (107 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312442|ref|YP_003776534.1| hypothetical protein Hsero_3142...   220   2e-59
gi|300312140|ref|YP_003776232.1| transcription regulator protein...   154   2e-39
gi|300313139|ref|YP_003777231.1| hypothetical protein Hsero_3845...    68   1e-13
gi|300312139|ref|YP_003776231.1| hypothetical protein Hsero_2831...    66   6e-13

>gi|300312442|ref|YP_003776534.1| hypothetical protein Hsero_3142
           [Herbaspirillum seropedicae SmR1]
          Length = 107

 Score =  220 bits (560), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 105/107 (98%), Positives = 107/107 (100%)

Query: 1   MAITLTEKAAKHISRYMERRGKGIGLRLGVRTTGCSGLAYKLEYVDEQAAEDTVFESHGV 60
           MAITLTEKAAKHISRYMERRGKGIGLRLGVRTTGCSGLAYKLEYVDEQ++EDTVFESHGV
Sbjct: 1   MAITLTEKAAKHISRYMERRGKGIGLRLGVRTTGCSGLAYKLEYVDEQSSEDTVFESHGV 60

Query: 61  RVFVDPKSLPYIDGTELDFAREGLNEGFKFQNPNVKDECGCGESFRI 107
           RVFVDPKSLPYIDGTELDFAREGLNEGFKFQNPNVKDECGCGESFRI
Sbjct: 61  RVFVDPKSLPYIDGTELDFAREGLNEGFKFQNPNVKDECGCGESFRI 107


>gi|300312140|ref|YP_003776232.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 106

 Score =  154 bits (389), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 68/107 (63%), Positives = 84/107 (78%), Gaps = 1/107 (0%)

Query: 1   MAITLTEKAAKHISRYMERRGKGIGLRLGVRTTGCSGLAYKLEYVDEQAAEDTVFESHGV 60
           M+ITLTE AA+ +  ++ +R   +GLRL V+T+GCSG+AY LEY D    +D  FESHGV
Sbjct: 1   MSITLTENAARRVHAFLAKR-SAVGLRLAVKTSGCSGMAYALEYADVAEPQDVRFESHGV 59

Query: 61  RVFVDPKSLPYIDGTELDFAREGLNEGFKFQNPNVKDECGCGESFRI 107
            V +DPKSLPY+DGTELDF REGLNEGFKF NPN K++CGCGESF +
Sbjct: 60  TVLIDPKSLPYLDGTELDFVREGLNEGFKFNNPNAKNQCGCGESFAV 106


>gi|300313139|ref|YP_003777231.1| hypothetical protein Hsero_3845
           [Herbaspirillum seropedicae SmR1]
          Length = 121

 Score = 68.2 bits (165), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/106 (31%), Positives = 55/106 (51%), Gaps = 1/106 (0%)

Query: 3   ITLTEKAAKHISRYMERRGK-GIGLRLGVRTTGCSGLAYKLEYVDEQAAEDTVFESHGVR 61
           I  ++ AA  +++ +E  G   + LR+ V+  GCSG  Y   + +    +DT    +GV+
Sbjct: 16  INFSDSAAAKVAQLIEEEGNPDLKLRVFVQGGGCSGFQYGFTFDEIVNEDDTTMSKNGVQ 75

Query: 62  VFVDPKSLPYIDGTELDFAREGLNEGFKFQNPNVKDECGCGESFRI 107
           + +D  S  Y+ G E+D+  +     F  +NPN    CGCG SF +
Sbjct: 76  LLIDSMSYQYLVGAEIDYKDDLEGAQFVIKNPNATTTCGCGSSFSV 121


>gi|300312139|ref|YP_003776231.1| hypothetical protein Hsero_2831
           [Herbaspirillum seropedicae SmR1]
          Length = 118

 Score = 65.9 bits (159), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 56/108 (51%), Gaps = 5/108 (4%)

Query: 3   ITLTEKAAKHISRYMERRGKG-IGLRLGVRTTGCSGLAYKLEYVDEQAAEDTVFESHGVR 61
           +  T+ A   +S  +   G   + LR+ V   GCSG  Y   + D    +D   E +GV 
Sbjct: 13  LIFTDSAVAKVSELISEEGNTELKLRIYVSGGGCSGFEYGFAFDDAVNEDDFCIERNGVS 72

Query: 62  VFVDPKSLPYIDGTELDFAREGLNEGFKF--QNPNVKDECGCGESFRI 107
           + VD  S+ Y++G E+ +  EGL EG +F  +NPN    CGCG SF +
Sbjct: 73  LLVDAMSMQYLNGAEIGY-EEGL-EGSRFIIKNPNATTTCGCGSSFSV 118


  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
   0.319    0.139    0.410 

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: 324,910
Number of extensions: 11943
Number of successful extensions: 29
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 29
Number of HSP's successfully gapped: 4
Length of query: 107
Length of database: 1,619,870
Length adjustment: 72
Effective length of query: 35
Effective length of database: 1,278,950
Effective search space: 44763250
Effective search space used: 44763250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 124 (52.4 bits)