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= 0002.0235.p
         (268 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...   322   2e-89
gi|300309880|ref|YP_003773972.1| IclR family transcription regul...   120   2e-28

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

 Score =  322 bits (825), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 194/240 (80%), Positives = 205/240 (85%)

Query: 1   LLAAARPLPLGDLARLAGMPAAKAFPHLVSLQKIGMLARDAQGNFFPGALALDLGLAALQ 60
           LLAA RPL LGDLARLAGMPAAKAFPHLVSLQKIG+L RDAQGNF PGAL L+LGLAALQ
Sbjct: 34  LLAAGRPLALGDLARLAGMPAAKAFPHLVSLQKIGLLMRDAQGNFLPGALGLELGLAALQ 93

Query: 61  RLSPLREAEAEVVTLVQATGLSVALAVVGPLGPTVVRLEESSRPQHVSLRIGTVLSMVHT 120
           RLSPLREAEAEV  L Q TGLSVALAV GPLGPTVVRLEESSRPQHVSLRIGTVLSMVHT
Sbjct: 94  RLSPLREAEAEVAALAQETGLSVALAVAGPLGPTVVRLEESSRPQHVSLRIGTVLSMVHT 153

Query: 121 AIGRVCAAHLPPDMLAGALAMDAIRMEGAQPDSVSHPDGSLRHDYAERLRQIRTLSLDQA 180
           AIGRVCAA  P D L GALA+D IRMEGA  +SV H DGSL   YA +L +IR   +DQA
Sbjct: 154 AIGRVCAACAPADGLPGALALDGIRMEGAALESVCHADGSLHAAYAAQLAKIRAQGMDQA 213

Query: 181 LGRPVPGIHTLAAPVFNHAGQLALVMAVMGSSGSFDTAADGVVARLLRAAAHNVSWRLGA 240
           LG PVPGI+TLAAPVFNHAGQLALVMAVMGSSGS+DTA  G VA+ LR+AA  VSWRLGA
Sbjct: 214 LGHPVPGINTLAAPVFNHAGQLALVMAVMGSSGSYDTALQGAVAQRLRSAAQAVSWRLGA 273


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

 Score =  120 bits (300), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 92/242 (38%), Positives = 136/242 (56%), Gaps = 19/242 (7%)

Query: 2   LAAAR-PLPLGDLARLAGMPAAKAFPHLVSLQKIGMLARD-AQGNFFPGALALDLGLAAL 59
           LAAAR P+PL  LA  AG+ +A+A  +LVSL ++G++ R  A+G++  G LAL LG+A L
Sbjct: 25  LAAARQPMPLVALAAAAGLTSAQAHTYLVSLLRLGLIKRTPAEGHYEAGPLALRLGVARL 84

Query: 60  QRLSPLREAEAEVVTLVQATGLSVALAVVGPLGPTVVRLEESSRPQHVSLRIGTVLSMVH 119
            +    R A A+   L  ATG SVA+++  P GPT+V    + +  H++L +G+V+++  
Sbjct: 85  SQQPAYRLAIAQAQHLSAATGCSVAVSLPTPEGPTIVHYAHAGKSLHLNLHVGSVMALAD 144

Query: 120 TAIGRVCAAHLPPDMLAGALAMDAIRMEGAQPDSVSHPDGS---LRHDYAERLRQIRTLS 176
           TA GR C A  PP     A                 HP+ S   +R   AE L  IR   
Sbjct: 145 TATGRTCCAFQPPQQWLPAWERQ-------------HPEASRARIRQFQAE-LEAIRQRG 190

Query: 177 LDQALGRPVPGIHTLAAPVFNHAGQLALVMAVMGSSGSFDTAADGVVARLLRAAAHNVSW 236
           L++A+  P PG+ +L  P+ +    L+L++ V+G SGS DT   G VAR LRA   ++S 
Sbjct: 191 LERAIDAPSPGVSSLCMPLLDQDQVLSLLLTVIGPSGSIDTGWRGAVARELRACIASISS 250

Query: 237 RL 238
           +L
Sbjct: 251 QL 252


  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
   0.319    0.133    0.382 

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: 861,772
Number of extensions: 35477
Number of successful extensions: 172
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 173
Number of HSP's successfully gapped: 2
Length of query: 268
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 184
Effective length of database: 1,222,130
Effective search space: 224871920
Effective search space used: 224871920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 130 (54.7 bits)