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= 0002.0597.p
         (141 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310712|ref|YP_003774804.1| transcription elongation factor...   211   1e-56
gi|300311440|ref|YP_003775532.1| transcription elongation/transc...    80   6e-17

>gi|300310712|ref|YP_003774804.1| transcription elongation factor
           protein [Herbaspirillum seropedicae SmR1]
          Length = 158

 Score =  211 bits (538), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 110/130 (84%), Positives = 121/130 (93%), Gaps = 2/130 (1%)

Query: 12  NAEYXPRAQGDLSENAEYDAAKERQAFIEGRIADLEGKLGSSLIVDPATLSSGADGRVVF 71
           NA    RAQGDLSENAEY++AKERQAFIEGRIADLEGKLG++ IVDPA L+  A+GRVVF
Sbjct: 31  NAIAEARAQGDLSENAEYESAKERQAFIEGRIADLEGKLGAAQIVDPAELN--AEGRVVF 88

Query: 72  AATVDLENLDSGEKVTYQIVGIDEADIKVSKVSVTSPIARALIGKSAGDVVAVEAPSGVR 131
           A+TVDLENLDSGEKVTYQIVG+DEADIK SKVSVTSPIARALIGKSAGDVVAVEAPSG++
Sbjct: 89  ASTVDLENLDSGEKVTYQIVGLDEADIKESKVSVTSPIARALIGKSAGDVVAVEAPSGLK 148

Query: 132 EYEILKVRYV 141
           EYEIL+VRYV
Sbjct: 149 EYEILEVRYV 158


>gi|300311440|ref|YP_003775532.1| transcription
           elongation/transcript cleavage factor protein
           [Herbaspirillum seropedicae SmR1]
          Length = 185

 Score = 80.1 bits (196), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 50/122 (40%), Positives = 72/122 (59%), Gaps = 3/122 (2%)

Query: 19  AQGDLSENAEYDAAKERQAFIEGRIADLEGKLGSSLIVDPATLSSGADGRVVFAATVDLE 78
           + GD SEN +Y   K+R   I+ RI  L  +L ++ +VDP ++  G+D ++ F ATV  E
Sbjct: 63  SNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDP-SVHHGSD-QIFFGATVTYE 120

Query: 79  NLDSGEKVTYQIVGIDEADIKVSKVSVTSPIARALIGKSAGDVVAVEAPSGVREYEILKV 138
           N   GE  T  IVGIDE D    ++S  SP+ARAL     GD V ++ P+G+ +  IL+V
Sbjct: 121 N-QRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTPAGLEQLTILEV 179

Query: 139 RY 140
            Y
Sbjct: 180 SY 181


  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
   0.310    0.131    0.346 

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: 412,790
Number of extensions: 15705
Number of successful extensions: 53
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 51
Number of HSP's successfully gapped: 2
Length of query: 141
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 65
Effective length of database: 1,260,010
Effective search space: 81900650
Effective search space used: 81900650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 126 (53.1 bits)