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= 0004.0097.p
         (255 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313880|ref|YP_003777972.1| transcription regulator protein...   104   6e-24
gi|300312279|ref|YP_003776371.1| GntR family transcription regul...   102   3e-23

>gi|300313880|ref|YP_003777972.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  104 bits (260), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 70/197 (35%), Positives = 104/197 (52%), Gaps = 7/197 (3%)

Query: 8   PAFVRLARYIHDRIIAGEWLPGQVLPGEEALAQDMKVSVGTVRKAFDVLSGQGLVTRHRG 67
           P +++L   +  +I A +W PGQ +P E  L+Q  +V+VGTVR+A + L  +GLV R  G
Sbjct: 12  PLYLQLRDLLATQIRAQKWQPGQPIPSEAELSQTYQVAVGTVRRAIETLMAEGLVERTHG 71

Query: 68  RGTFVTRATNERAFTSFYRLTDRADGVRRLPQDTLLLRERVAADADERAALKLDAGALVY 127
           RGTFV +A  + +   F+R  + ADG    P+  ++ R+ V A A    AL+L   A V 
Sbjct: 72  RGTFVRKARFDNSLFRFFRF-ESADGRPLAPKSVIVSRKLVEAPAQAAEALQLKPHAKVI 130

Query: 128 RLRRLRVLDDTPLVLETISFPFARVGNKEWGADGAPFH---LVYSFLEQQCGISVSRVED 184
            L RLR++D  P++ E I     R       AD AP     L+Y   E++CG+ V+   +
Sbjct: 131 ELHRLRMVDGQPVLAENIYLCAQRFKAL---ADKAPEEFGDLLYPLYERECGLIVASARE 187

Query: 185 RLRACLLPKKVAKDFGL 201
            L    +    AK  GL
Sbjct: 188 TLTVETVTAAQAKLLGL 204


>gi|300312279|ref|YP_003776371.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 334

 Score =  102 bits (254), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 69/213 (32%), Positives = 109/213 (51%), Gaps = 8/213 (3%)

Query: 6   LSPAFVRLARYIHDRIIAGEWLPGQVLPGEEALAQDMKVSVGTVRKAFDVLSGQGLVTRH 65
            SP + ++   I  R+ AGEW PG+++P E  L    KVS GTVRKA D L+ + LV R 
Sbjct: 100 FSPLYQQIKALIMQRLEAGEWKPGELIPSEVELGSRFKVSQGTVRKAIDELAAENLVVRR 159

Query: 66  RGRGTFVTRATNERAFTSFYRLTDRADGVRRLPQDTLLLRERVAADADERAALKLDAGAL 125
           +G+GTFV      +A   F RL   +D  +R P++ ++  +RV A A+    L + +G  
Sbjct: 160 QGKGTFVATHHETQAQFRFLRLMADSDEPQR-PENKIIEVKRVRASAEVARQLDMKSGDS 218

Query: 126 VYRLRRLRVLDDTPLVLETISFP---FARVGNKEWGADGAPFHLVYSFLEQQCGISVSRV 182
           V  +RR++  +  P++LE I  P   F  +  +       P   +Y   E + G  + R 
Sbjct: 219 VIFIRRVKSFNGVPIILEDIWLPGAIFKGLTAERLVEYRGP---LYGLFESEFGTRMIRA 275

Query: 183 EDRLRACLLPKKVAKDFGL-PAGPLPAAIRSCW 214
           E+R+RA       A+  G+ P  PL +  R+ +
Sbjct: 276 EERIRAVGADPDAAEFLGVTPQTPLLSVERASF 308


  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
   0.324    0.138    0.430 

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: 742,157
Number of extensions: 27742
Number of successful extensions: 128
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 172
Effective length of database: 1,226,865
Effective search space: 211020780
Effective search space used: 211020780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 129 (54.3 bits)