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= 0001.0527.p
         (286 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309881|ref|YP_003773973.1| transcription regulator protein...   354   5e-99
gi|300309880|ref|YP_003773972.1| IclR family transcription regul...   138   5e-34

>gi|300309881|ref|YP_003773973.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 282

 Score =  354 bits (908), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 216/275 (78%), Positives = 227/275 (82%)

Query: 5   KDLPLPEAADPEGARSQRGIQSLDSSGALLDALLEAACPLPLGDLARLAGMPAAKAFPHL 64
           K LP  +A     AR QRGIQSLD++G LLDALL A  PL LGDLARLAGMPAAKAFPHL
Sbjct: 2   KHLPPDDAPADSDARGQRGIQSLDNTGQLLDALLAAGRPLALGDLARLAGMPAAKAFPHL 61

Query: 65  VSLQKIGLLARDAQGNFFPGPLSLELGLAALQRLSPLREAEAEVATLAQATGLSVALAVF 124
           VSLQKIGLL RDAQGNF PG L LELGLAALQRLSPLREAEAEVA LAQ TGLSVALAV 
Sbjct: 62  VSLQKIGLLMRDAQGNFLPGALGLELGLAALQRLSPLREAEAEVAALAQETGLSVALAVA 121

Query: 125 GPLGPTVVRLEESSRPQHVSLRIGTVLSMVHTAIGRVCAAYLPADMLAGALAMDAIRMEG 184
           GPLGPTVVRLEESSRPQHVSLRIGTVLSMVHTAIGRVCAA  PAD L GALA+D IRMEG
Sbjct: 122 GPLGPTVVRLEESSRPQHVSLRIGTVLSMVHTAIGRVCAACAPADGLPGALALDGIRMEG 181

Query: 185 AQPDSVSHPDGSLRHDYAQRLEQVRTQRLDQALGRPVPGINTLAAPVFNHTGQLALVMAV 244
           A  +SV H DGSL   YA +L ++R Q +DQALG PVPGINTLAAPVFNH GQLALVMAV
Sbjct: 182 AALESVCHADGSLHAAYAAQLAKIRAQGMDQALGHPVPGINTLAAPVFNHAGQLALVMAV 241

Query: 245 MGSSGSYDPRYEGDVAQLLRAAAHTVSWRLGAFDD 279
           MGSSGSYD   +G VAQ LR+AA  VSWRLGA  D
Sbjct: 242 MGSSGSYDTALQGAVAQRLRSAAQAVSWRLGAALD 276


>gi|300309880|ref|YP_003773972.1| IclR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 257

 Score =  138 bits (347), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 97/262 (37%), Positives = 154/262 (58%), Gaps = 18/262 (6%)

Query: 18  ARSQRGIQSLDSSGALLDALLEAACPLPLGDLARLAGMPAAKAFPHLVSLQKIGLLARD- 76
           A++QRGIQS++ +G LL AL  A  P+PL  LA  AG+ +A+A  +LVSL ++GL+ R  
Sbjct: 6   AKTQRGIQSVEVAGRLLQALAAARQPMPLVALAAAAGLTSAQAHTYLVSLLRLGLIKRTP 65

Query: 77  AQGNFFPGPLSLELGLAALQRLSPLREAEAEVATLAQATGLSVALAVFGPLGPTVVRLEE 136
           A+G++  GPL+L LG+A L +    R A A+   L+ ATG SVA+++  P GPT+V    
Sbjct: 66  AEGHYEAGPLALRLGVARLSQQPAYRLAIAQAQHLSAATGCSVAVSLPTPEGPTIVHYAH 125

Query: 137 SSRPQHVSLRIGTVLSMVHTAIGRVCAAYLPADMLAGALAMDAIRMEGAQPDSVSHPDGS 196
           + +  H++L +G+V+++  TA GR C A+ P      A                 HP+ S
Sbjct: 126 AGKSLHLNLHVGSVMALADTATGRTCCAFQPPQQWLPAWERQ-------------HPEAS 172

Query: 197 ---LRHDYAQRLEQVRTQRLDQALGRPVPGINTLAAPVFNHTGQLALVMAVMGSSGSYDP 253
              +R   A+ LE +R + L++A+  P PG+++L  P+ +    L+L++ V+G SGS D 
Sbjct: 173 RARIRQFQAE-LEAIRQRGLERAIDAPSPGVSSLCMPLLDQDQVLSLLLTVIGPSGSIDT 231

Query: 254 RYEGDVAQLLRAAAHTVSWRLG 275
            + G VA+ LRA   ++S +L 
Sbjct: 232 GWRGAVARELRACIASISSQLN 253


  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
   0.318    0.134    0.387 

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: 853,041
Number of extensions: 32627
Number of successful extensions: 156
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 3
Length of query: 286
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 202
Effective length of database: 1,222,130
Effective search space: 246870260
Effective search space used: 246870260
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 (21.7 bits)
S2: 130 (54.7 bits)