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= 0250.0004.p
         (458 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies...   410   e-116
gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil...    63   6e-11
gi|300310169|ref|YP_003774261.1| methyl-accepting chemotaxis tra...    59   8e-10

>gi|300313993|ref|YP_003778085.1| diguanylate
           cyclase/phosphodiesterase with PAS/PAC sensor
           domain-containing protein [Herbaspirillum seropedicae
           SmR1]
          Length = 573

 Score =  410 bits (1055), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 208/413 (50%), Positives = 300/413 (72%), Gaps = 1/413 (0%)

Query: 2   LDLLSLKLLRRIEIRYRLINSFLLVSMLPLVIAGIVAYRESSSASQEKVRIFAAELVKQV 61
           LD LS   LRRI I YRLI++F+LVS+LPL+I+G++AY E+S A+Q+KVR ++ ++V+Q+
Sbjct: 5   LDFLSRHFLRRIAIGYRLISAFILVSLLPLLISGLLAYGETSRATQDKVRAYSVQVVQQI 64

Query: 62  AQNMLQQIEKIESSSEELAMSERMQNALAGYYSKNPAERAAGHGEIIRLLLENYGSFEYV 121
           +QN+L ++EKIE +SE LA+SE+MQ  LA YYS +    AA      R+LL+ YG+  YV
Sbjct: 65  SQNLLLRMEKIEDTSEALALSEKMQRLLADYYSGDADASAAARNSAARVLLDTYGALTYV 124

Query: 122 NQKYVLDRRHRIMDPQVFAQLGDGVARFAEDAPDMKGRPYWDVYSTAAGQNSVVMLRDIL 181
           NQKY+LDR  +++DPQ+FA L   + R AE+AP++ GR +W +Y    GQ S+ MLR++ 
Sbjct: 125 NQKYLLDRDRQVIDPQIFAPLASSIGRVAEEAPELTGRGWWTLYHAGHGQKSLAMLREVR 184

Query: 182 FKSNNRVAGTLFVGLRPLHFSRIFESVNLGYGSRMLVIDARDGHVIVSANAADGNAPESG 241
           F +NNR AG LFVG+ P +F  IF   +LGYG+ + ++DA DG V+V +  +  +  +  
Sbjct: 185 FTANNRPAGVLFVGVHPSYFFDIFRGADLGYGASISIVDASDGAVVVQSRESSASQADPA 244

Query: 242 LVVAVARNVAEGRD-NFVSYRDGDNKQQLAAFAPVPHTNWMVVNITPLNALNTEVRSIRN 300
           L+  +  ++A+GRD +F++Y   D     AA A +PHT+W V +ITP + LN + RS+R+
Sbjct: 245 LLGGITESLAQGRDSDFIAYVGADKTPYYAAIARLPHTSWWVASITPSDRLNADTRSVRD 304

Query: 301 KIIAIGVLCFILALVLSFIIARSISLPLKQLVGVMKATRTGNYLIRMDYEGRDEIAVLSQ 360
           KIIAIG++CF ++L+LS +I+RSIS+PL++LV  MK   +G+  +R++  G DEIAVLS+
Sbjct: 305 KIIAIGLVCFAVSLLLSALISRSISVPLQRLVAAMKEAGSGDTTVRVEQHGNDEIAVLSR 364

Query: 361 RFNEMASKVHQHNERLEELVAERTRELEQANHQLEALSATDSLTGIANRRRFD 413
           +FNEMA K+ Q+ E LEE V  RTRELE+AN +LEALSATD LTG+ANRRRFD
Sbjct: 365 KFNEMAGKLQQNREVLEEQVRLRTRELERANRKLEALSATDGLTGVANRRRFD 417


>gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family
           protein [Herbaspirillum seropedicae SmR1]
          Length = 369

 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 66/145 (45%), Gaps = 37/145 (25%)

Query: 300 NKIIAIGVLCFILALVLSFIIARSISLPLKQLVGV--------MKATRTGNYLIRMDYEG 351
           N +I   VL FI      ++  R +  P+ +L           M+  R+    I +    
Sbjct: 78  NSVIKTLVLWFIFL----YVFRRWLGQPITRLADFVRELDLNQMETPRS----IHLPGRR 129

Query: 352 RDEIAVLSQRFNEMASKVHQH---------------------NERLEELVAERTRELEQA 390
           R E+  L+   N M +K+H+H                     N  LE  +AERTR+L QA
Sbjct: 130 RHELHFLADAINLMLAKLHRHTIHNHALYKELEQEKQSLSALNRSLELRIAERTRDLAQA 189

Query: 391 NHQLEALSATDSLTGIANRRRFDXS 415
           N QL +LS TD LTGIANRR FD +
Sbjct: 190 NEQLRSLSLTDGLTGIANRRSFDET 214


>gi|300310169|ref|YP_003774261.1| methyl-accepting chemotaxis
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 657

 Score = 58.9 bits (141), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 52/226 (23%), Positives = 97/226 (42%), Gaps = 26/226 (11%)

Query: 205 FESVNLGYGSRMLVIDARDGH---VIVSANAADGNAPESGLVV-------AVARNVAEGR 254
            +++ +G       ++AR+G    V+++  A +G    S L+           + + + +
Sbjct: 228 IKALKIGDTGNFFALNAREGKDLGVMIAGAAREGKEEGSSLLELKDAAGDTYIKTMLQQK 287

Query: 255 DNFVSYRDGDNKQQLAAFAPVPHTNWMVVNITPLNALNTEVRSIRNKIIAIGVLCF-ILA 313
           D  + Y   D ++++ AF   P  +W++     ++ +  EV S+RN  I +G+L   +LA
Sbjct: 288 DGSLPYTAADGRKKILAFTYYPGWHWVIAGEAAVDEITREVSSMRNLYIGLGLLFLAVLA 347

Query: 314 LVLSFIIARSISLPLKQLVGVMKATRTGNYLIRMDYEGRDEIAVLSQRFN-------EMA 366
            +L+ ++ R +S PL  +        +G+   R+     DEI  L   FN       E+ 
Sbjct: 348 AILTVMVNRMVSRPLDAVCQAADRIASGDLTTRLHVHSSDEIGRLMGAFNGISMGLSEVV 407

Query: 367 SKVHQHNERLEELVAE--------RTRELEQANHQLEALSATDSLT 404
           S V    E +    +E          R  +QA    E  SA + LT
Sbjct: 408 SSVRAGTEEINTAASEIASGNLNLSVRTEQQAGALEETASAMEELT 453


  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
   0.320    0.133    0.375 

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: 1,145,632
Number of extensions: 44353
Number of successful extensions: 237
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 241
Number of HSP's successfully gapped: 3
Length of query: 458
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 370
Effective length of database: 1,203,190
Effective search space: 445180300
Effective search space used: 445180300
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 (21.9 bits)
S2: 132 (55.5 bits)