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/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152981655|ref|YP_001353015.1| transcription elongation factor...   289   7e-80
gi|152981797|ref|YP_001351733.1| transcription elongation factor...   169   1e-43
gi|152980351|ref|YP_001353931.1| GreA transcription elongation f...   101   4e-23

>gi|152981655|ref|YP_001353015.1| transcription elongation factor
           GreB [Janthinobacterium sp. Marseille]
          Length = 183

 Score =  289 bits (740), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 137/173 (79%), Positives = 155/173 (89%)

Query: 13  DDDDELALPAIPAGAKNYMTPQGHARIKDELLHLIDEERPEVVRVVSWAASNGDRSENGD 72
           D+D + + P IPAGAKNYMTPQGH R+K ELL LID ERPEVV++VSWAASNGDRSENGD
Sbjct: 11  DEDGDNSAPPIPAGAKNYMTPQGHLRMKTELLKLIDVERPEVVQIVSWAASNGDRSENGD 70

Query: 73  YLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQVFFGATVHYENQRGEAHTVTIV 132
           Y+YGK+RLR+ID RIRFLTKRLD AEVVDPS+HHGSDQ+FFGATV YE Q G+ HTVTI+
Sbjct: 71  YIYGKRRLRQIDGRIRFLTKRLDLAEVVDPSIHHGSDQIFFGATVRYETQAGDEHTVTIL 130

Query: 133 GIDELDPLKGRISWISPVARALTKAREGDEVVLQTPSGVEQLTILEVSYPAPQ 185
           GIDELDPL G+ISWISPVARALTKAREGD VVL+TP G+E+L ILEV+YPAPQ
Sbjct: 131 GIDELDPLNGKISWISPVARALTKAREGDTVVLKTPGGLEELLILEVTYPAPQ 183


>gi|152981797|ref|YP_001351733.1| transcription elongation factor
           GreB [Janthinobacterium sp. Marseille]
          Length = 175

 Score =  169 bits (427), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 94/184 (51%), Positives = 125/184 (67%), Gaps = 12/184 (6%)

Query: 1   MNKAFVKESDGGDDDDELAL-PAIPAGAKNYMTPQGHARIKDELLHLIDEERPEVVRVVS 59
           MNKAFVKE++   DDD L L P +P G +NY+TP G+  ++ EL  L+D  RP       
Sbjct: 1   MNKAFVKETN---DDDVLPLVPEMPVGVRNYITPDGYRHLQQELQQLLDVARP------- 50

Query: 60  WAASNGDRSENGDYLYGKKRLREIDRRIRFLTKRLDNAEVVDPSVHHGSDQVFFGATVHY 119
            AA   D ++       +  LREI++RI +L  R+++AEVVD SVH   D++FFGA+V Y
Sbjct: 51  -AAMQMDAADTAMASAQEASLREIEQRIHYLQTRVESAEVVDASVHADGDRIFFGASVDY 109

Query: 120 ENQRGEAHTVTIVGIDELDPLKGRISWISPVARALTKAREGDEVVLQTPSGVEQLTILEV 179
           EN  GE HT TIVG+DELDP +GRISW+SP+A++L  A EGD V+LQTP+G E+L +L V
Sbjct: 110 ENTAGETHTATIVGLDELDPAQGRISWLSPLAQSLLGAEEGDTVLLQTPAGPEELHVLTV 169

Query: 180 SYPA 183
            YPA
Sbjct: 170 RYPA 173


>gi|152980351|ref|YP_001353931.1| GreA transcription elongation
           factor [Janthinobacterium sp. Marseille]
          Length = 157

 Score =  101 bits (251), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 58/152 (38%), Positives = 89/152 (58%), Gaps = 1/152 (0%)

Query: 31  MTPQGHARIKDELLHLIDEERPEVVRVVSWAASNGDRSENGDYLYGKKRLREIDRRIRFL 90
           +TP G   +K+EL  L  +ERP V+  ++ A + GD SEN DY   K++   I+ RI  +
Sbjct: 5   ITPYGANVLKEELHRLKTKERPWVINAIAEARAQGDLSENADYDAAKEKQSFIEGRIADI 64

Query: 91  TKRLDNAEVVDPSVHHGSDQVFFGATVHYEN-QRGEAHTVTIVGIDELDPLKGRISWISP 149
             +L  ++V+DP+      +V F ATV  E+ + GE  T  IVGIDE D  + ++S  SP
Sbjct: 65  EGKLGTSQVIDPTTLEAEGRVVFAATVDLEDLESGEKVTYQIVGIDEADLKEKKVSITSP 124

Query: 150 VARALTKAREGDEVVLQTPSGVEQLTILEVSY 181
           +ARA+     GD V ++ P+G+ +  IL+V Y
Sbjct: 125 IARAMIGKYAGDVVGVEAPAGLREYEILQVRY 156


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
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: 3697
Number of Hits to DB: 476,096
Number of extensions: 20004
Number of successful extensions: 42
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 39
Number of HSP's successfully gapped: 3
Length of query: 185
Length of database: 1,221,021
Length adjustment: 78
Effective length of query: 107
Effective length of database: 932,655
Effective search space: 99794085
Effective search space used: 99794085
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: 127 (53.5 bits)