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= 0005.0224.p
         (176 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...   287   4e-79
gi|300310712|ref|YP_003774804.1| transcription elongation factor...    92   3e-20

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

 Score =  287 bits (734), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 144/169 (85%), Positives = 159/169 (94%), Gaps = 1/169 (0%)

Query: 8   MNKAFVKESDGDDDDE-LALPAIPAGTRNYMTPAGHKRIKDELLHLIDVDRPEVVRIVHW 66
           MNKAFVKESDGDDDDE +ALP++PAG++NYMTP GH+RIKDELLHLID +RPEVVR+V W
Sbjct: 1   MNKAFVKESDGDDDDEDIALPSVPAGSKNYMTPQGHQRIKDELLHLIDEERPEVVRVVSW 60

Query: 67  AASNGDRSENGDYIYGKRRLREIDRRIRFLTKRLDIAEVVDPTIHHGNDQIFFGATVTYE 126
           AASNGDRSENGDY+YGK+RLREIDRRIRFLTKRLD AEVVDP++HHG+DQIFFGATVTYE
Sbjct: 61  AASNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQIFFGATVTYE 120

Query: 127 NQDGIAHTVTIVGIDELDPLNGKISWISPVARTLTKAREGDEVTLQTPS 175
           NQ G AHTVTIVGIDELDPL G+ISWISPVAR LTKAREGDEV LQTP+
Sbjct: 121 NQRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTPA 169


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

 Score = 91.7 bits (226), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 55/140 (39%), Positives = 76/140 (54%), Gaps = 1/140 (0%)

Query: 37  MTPAGHKRIKDELLHLIDVDRPEVVRIVHWAASNGDRSENGDYIYGKRRLREIDRRIRFL 96
           +T  G + +K+EL  L   DRPEV+  +  A + GD SEN +Y   K R   I+ RI  L
Sbjct: 6   LTKRGAELLKEELHRLKTKDRPEVINAIAEARAQGDLSENAEYESAKERQAFIEGRIADL 65

Query: 97  TKRLDIAEVVDPTIHHGNDQIFFGATVTYENQD-GIAHTVTIVGIDELDPLNGKISWISP 155
             +L  A++VDP   +   ++ F +TV  EN D G   T  IVG+DE D    K+S  SP
Sbjct: 66  EGKLGAAQIVDPAELNAEGRVVFASTVDLENLDSGEKVTYQIVGLDEADIKESKVSVTSP 125

Query: 156 VARTLTKAREGDEVTLQTPS 175
           +AR L     GD V ++ PS
Sbjct: 126 IARALIGKSAGDVVAVEAPS 145


  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
   0.317    0.136    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: 572,632
Number of extensions: 22615
Number of successful extensions: 47
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 45
Number of HSP's successfully gapped: 2
Length of query: 176
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 97
Effective length of database: 1,245,805
Effective search space: 120843085
Effective search space used: 120843085
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: 41 (21.6 bits)
S2: 127 (53.5 bits)