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= 0001.1978.p
         (185 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311440|ref|YP_003775532.1| transcription elongation/transc...   348   2e-97
gi|300310712|ref|YP_003774804.1| transcription elongation factor...   107   9e-25

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

 Score =  348 bits (892), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 173/185 (93%), Positives = 182/185 (98%)

Query: 1   MNKAFVKESDGGDDDDELALPAIPAGAKNYMTPQGHARIKDELLHLIDEERPEVVRVVSW 60
           MNKAFVKESDG DDD+++ALP++PAG+KNYMTPQGH RIKDELLHLIDEERPEVVRVVSW
Sbjct: 1   MNKAFVKESDGDDDDEDIALPSVPAGSKNYMTPQGHQRIKDELLHLIDEERPEVVRVVSW 60

Query: 61  AASNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQVFFGATVHYE 120
           AASNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQ+FFGATV YE
Sbjct: 61  AASNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQIFFGATVTYE 120

Query: 121 NQRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTPSGVEQLTILEVS 180
           NQRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTP+G+EQLTILEVS
Sbjct: 121 NQRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTPAGLEQLTILEVS 180

Query: 181 YPAPQ 185
           YPAPQ
Sbjct: 181 YPAPQ 185


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

 Score =  107 bits (266), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 61/152 (40%), Positives = 91/152 (59%), Gaps = 1/152 (0%)

Query: 31  MTPQGHARIKDELLHLIDEERPEVVRVVSWAASNGDRSENGDYLYGKKRLREIDRRIRFL 90
           +T +G   +K+EL  L  ++RPEV+  ++ A + GD SEN +Y   K+R   I+ RI  L
Sbjct: 6   LTKRGAELLKEELHRLKTKDRPEVINAIAEARAQGDLSENAEYESAKERQAFIEGRIADL 65

Query: 91  TKRLDNAEVVDPSVHHGSDQVFFGATVHYEN-QRGEAHTVTIVGIDELDPLKGRISWISP 149
             +L  A++VDP+  +   +V F +TV  EN   GE  T  IVG+DE D  + ++S  SP
Sbjct: 66  EGKLGAAQIVDPAELNAEGRVVFASTVDLENLDSGEKVTYQIVGLDEADIKESKVSVTSP 125

Query: 150 VARALTKAREGDEVVLQTPSGVEQLTILEVSY 181
           +ARAL     GD V ++ PSG+++  ILEV Y
Sbjct: 126 IARALIGKSAGDVVAVEAPSGLKEYEILEVRY 157


  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    0.135    0.391 

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: 640,931
Number of extensions: 27130
Number of successful extensions: 55
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 54
Number of HSP's successfully gapped: 2
Length of query: 185
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 105
Effective length of database: 1,241,070
Effective search space: 130312350
Effective search space used: 130312350
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: 128 (53.9 bits)