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= 0001.1173.p
         (332 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310694|ref|YP_003774786.1| MerR-family transcription regul...   386   e-108
gi|300309757|ref|YP_003773849.1| hypothetical protein Hsero_0416...   162   4e-41

>gi|300310694|ref|YP_003774786.1| MerR-family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 330

 Score =  386 bits (991), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 214/336 (63%), Positives = 254/336 (75%), Gaps = 15/336 (4%)

Query: 1   MTSKPLPTEDSPDLSDLPLLRPGAVARQLGMSVETLRAWEHRYGLTSSQHSGGGQRLYSQ 60
           MTS   PT D  +L++LPLLRPGAVARQLGMSVETLRAWE+RYGLTSS HSGGGQRLYSQ
Sbjct: 1   MTSNS-PT-DPDELNELPLLRPGAVARQLGMSVETLRAWENRYGLTSSHHSGGGQRLYSQ 58

Query: 61  EDLQRLGWIKKLGDAGHRIGKLATLTPQDLQALAQSLPAEHAAPPSTMAT-GGMRVPRLV 119
           ED+QRL  IK+L D GHRIG+LA L    L+AL    P+  AA P+   T  G+R   LV
Sbjct: 59  EDVQRLAHIKRLVDEGHRIGQLAALP---LEALKSLDPSPEAAGPAGQTTLAGLR---LV 112

Query: 120 LVGPWISTKASRQALTQQQFSITAAVETLEELDLPAFEAD----LLVLESAVLGHDLEDR 175
           L GPWIS+    +AL QQQ S++AAV+ LEEL   +   D    LL++ESAVL   L  R
Sbjct: 113 LAGPWISSTGCIEALRQQQASVSAAVQDLEELRQSSLGLDTGVALLLVESAVLDPGLGGR 172

Query: 176 LDSLHHSFIQVPVVILYRFGSPEMVARLVQAGHRLVRKAMDGIDVEWLCDLLKRVPLPTT 235
           ++S+  SF    VVILYRFGSPEMVARL QAGH+LVRK MDGID  WLC+L++R+ LP  
Sbjct: 173 MESVRRSFASARVVILYRFGSPEMVARLTQAGHQLVRKPMDGIDPAWLCELVRRLDLPPG 232

Query: 236 AHILGSAEESLPAPRFSESTLVAISEQSDQMQCECPRHLAELLTALIGFERYSRQCEDES 295
              + S +  +PAPRFSE+ L  +S+ S +MQCECPRHLAELLTAL+GFERYSRQCEDES
Sbjct: 233 EVQMDSPD--VPAPRFSEAELAQVSQASTRMQCECPRHLAELLTALVGFERYSRQCEDES 290

Query: 296 EQEAELHRALCIAAGQARLPLEEALQRLARVKGITL 331
           E+EA LHR LC+AAG+ARLPLEE LQRLA+VKGI+L
Sbjct: 291 EEEAALHRELCLAAGRARLPLEETLQRLAQVKGISL 326


>gi|300309757|ref|YP_003773849.1| hypothetical protein Hsero_0416
           [Herbaspirillum seropedicae SmR1]
          Length = 347

 Score =  162 bits (410), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 120/339 (35%), Positives = 175/339 (51%), Gaps = 16/339 (4%)

Query: 3   SKPLPTEDSPDLSD------LPLLRPGAVARQLGMSVETLRAWEHRYGLTSSQHSGGGQR 56
           ++P+PT  +   S        PL R GAVAR L M V TLR WE RY LT  Q S  GQR
Sbjct: 2   TEPIPTAPTSSTSSPEEKGPAPLRRTGAVARMLRMPVATLRVWERRYALTQGQLSPSGQR 61

Query: 57  LYSQEDLQRLGWIKKLGDAGHRIGKLATLTPQDLQALAQSLPAEHAAPPSTMATGGMRVP 116
           LYS+ D++RL  I++L + GH IG LA L  + LQ +A +    HA  P+       R  
Sbjct: 62  LYSEADVRRLALIRQLTELGHAIGSLAGLDMEQLQQVAATHAELHAGRPTPPEAVQGRW- 120

Query: 117 RLVLVGPWISTKASRQALTQ---QQFSITAAVETLEE--LDLPAFEADLLVLESAVLGHD 171
           RL ++G  ++ +  +  L Q   +   +    E +E+  + L   E D L+L    L   
Sbjct: 121 RLAVIGSTLAQRLDKPGLLQRLGRPLQLLGPFENIEQAAMALKREEVDALLLHEPQLHAG 180

Query: 172 LEDRLDSLHHSFIQVPVVILYRFGSPEMVARLVQAGHRLVRKAM-DGIDVEWLCDLLKRV 230
               L+S   +   +P+ +LY F S  +   L   G  L+R    D + ++WL  L   V
Sbjct: 181 WLGALESSAPALSGLPMAVLYGFASEAVCETLAAVGISLLRAPQPDVVILQWLRGL---V 237

Query: 231 PLPTTAHILGSAEESLPAPRFSESTLVAISEQSDQMQCECPRHLAELLTALIGFERYSRQ 290
            L + A    +A   LP  R+S++ L+A + QS  + CECPRH+AELL  L  FERYS Q
Sbjct: 238 ALSSPAREEMAAGTVLPPRRWSDNQLIAFANQSTTVACECPRHVAELLMQLSQFERYSAQ 297

Query: 291 CEDESEQEAELHRALCIAAGQARLPLEEALQRLARVKGI 329
           C + +  +A+LH+ L     ++R   E AL R+A  +G+
Sbjct: 298 CANRNVADAQLHQYLQQLTSESRQRFEMALTRIAEHEGL 336


  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    0.133    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: 994,797
Number of extensions: 40991
Number of successful extensions: 185
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 2
Length of query: 332
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 246
Effective length of database: 1,212,660
Effective search space: 298314360
Effective search space used: 298314360
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: 131 (55.1 bits)