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= 0082.0015.p
         (144 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...   220   4e-59
gi|300311440|ref|YP_003775532.1| transcription elongation/transc...    83   1e-17

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

 Score =  220 bits (560), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 112/131 (85%), Positives = 123/131 (93%), Gaps = 2/131 (1%)

Query: 1   MSTVPITKYGAELLKEELQRLKTKERPAVINAIAEARAQGDLSENAEYDAAKERQAFIEG 60
           MSTVP+TK GAELLKEEL RLKTK+RP VINAIAEARAQGDLSENAEY++AKERQAFIEG
Sbjct: 1   MSTVPLTKRGAELLKEELHRLKTKDRPEVINAIAEARAQGDLSENAEYESAKERQAFIEG 60

Query: 61  RIADLEGKLGSSLVVDPATLSSGADGRVVFAATVDLENLDSGEKVTYQIVGIDEADIKVS 120
           RIADLEGKLG++ +VDPA L+  A+GRVVFA+TVDLENLDSGEKVTYQIVG+DEADIK S
Sbjct: 61  RIADLEGKLGAAQIVDPAELN--AEGRVVFASTVDLENLDSGEKVTYQIVGLDEADIKES 118

Query: 121 KVSVTSPIARA 131
           KVSVTSPIARA
Sbjct: 119 KVSVTSPIARA 129


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

 Score = 82.8 bits (203), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 53/132 (40%), Positives = 77/132 (58%), Gaps = 3/132 (2%)

Query: 6   ITKYGAELLKEELQRLKTKERPAVINAIAEARAQGDLSENAEYDAAKERQAFIEGRIADL 65
           +T  G + +K+EL  L  +ERP V+  ++ A + GD SEN +Y   K+R   I+ RI  L
Sbjct: 31  MTPQGHQRIKDELLHLIDEERPEVVRVVSWAASNGDRSENGDYLYGKKRLREIDRRIRFL 90

Query: 66  EGKLGSSLVVDPATLSSGADGRVVFAATVDLENLDSGEKVTYQIVGIDEADIKVSKVSVT 125
             +L ++ VVDP ++  G+D ++ F ATV  EN   GE  T  IVGIDE D    ++S  
Sbjct: 91  TKRLDNAEVVDP-SVHHGSD-QIFFGATVTYEN-QRGEAHTVTIVGIDELDPLKGRISWI 147

Query: 126 SPIARAXCALRD 137
           SP+ARA    R+
Sbjct: 148 SPVARALTKARE 159


  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
   0.313    0.130    0.342 

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: 394,889
Number of extensions: 14422
Number of successful extensions: 59
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 57
Number of HSP's successfully gapped: 2
Length of query: 144
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 67
Effective length of database: 1,255,275
Effective search space: 84103425
Effective search space used: 84103425
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 (21.9 bits)
S2: 126 (53.1 bits)