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= 0002.0288.p
         (121 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [...   182   5e-48
gi|300314042|ref|YP_003778134.1| signal transduction protein con...    98   2e-22
gi|300309360|ref|YP_003773452.1| hypothetical protein Hsero_0014...    95   1e-21
gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies...    89   1e-19
gi|300312026|ref|YP_003776118.1| signal transduction protein con...    88   2e-19

>gi|300311871|ref|YP_003775963.1| EAL domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 1036

 Score =  182 bits (463), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 89/107 (83%), Positives = 96/107 (89%)

Query: 2   LDSPYQLGEVEYRTTASVGATVFRGRQASIDELLKQADLAMYKSKETGRNAISFFDPAMQ 61
           L S YQL +VEYRTTAS+GATVF GR AS+DEL+KQADLAMYK+KETGRNA+ FFDPAMQ
Sbjct: 711 LGSTYQLDDVEYRTTASIGATVFLGRAASVDELMKQADLAMYKAKETGRNALRFFDPAMQ 770

Query: 62  TVVLERAALEAGLRKAIDDGQLVLHYQAQVVEGGRVTGAEVLVRWQH 108
           T VLERA LEAGLRKAID  QL+LHYQ QVVEGGRVTGAEVLVRWQH
Sbjct: 771 TAVLERATLEAGLRKAIDGNQLLLHYQPQVVEGGRVTGAEVLVRWQH 817


>gi|300314042|ref|YP_003778134.1| signal transduction protein
           containing a membrane domain, an EAL and a GGDEF
           domain-containing protein [Herbaspirillum seropedicae
           SmR1]
          Length = 948

 Score = 98.2 bits (243), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 48/109 (44%), Positives = 65/109 (59%), Gaps = 1/109 (0%)

Query: 4   SPYQLGEVEYRTTASVGATVFRGRQASIDELLKQADLAMYKSKETGRNAISFFDPAMQTV 63
           +P  LG      T SVG   +       + L+K AD+AMY+ K+TGRN   F+ PAM   
Sbjct: 628 APVTLGGHTLFMTCSVGVACYPNDGTDGETLIKHADIAMYRGKQTGRNNFQFYTPAMNEQ 687

Query: 64  VLERAALEAGLRKAIDDGQLVLHYQAQV-VEGGRVTGAEVLVRWQHXRL 111
            LER  +E  LR A+D G+ +LHYQ +V +  GRV G+E L+RWQH +L
Sbjct: 688 ALERLRIEGDLRNALDHGEFLLHYQPKVDLASGRVIGSEALIRWQHPQL 736


>gi|300309360|ref|YP_003773452.1| hypothetical protein Hsero_0014
           [Herbaspirillum seropedicae SmR1]
          Length = 726

 Score = 95.1 bits (235), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/111 (43%), Positives = 67/111 (60%), Gaps = 3/111 (2%)

Query: 1   VLDS---PYQLGEVEYRTTASVGATVFRGRQASIDELLKQADLAMYKSKETGRNAISFFD 57
           +LD+   P  L    +  + ++G  + R  Q    EL+ QA+LAM +S+  GRN   FFD
Sbjct: 400 ILDAFTDPQSLSAARFPCSVNLGINIVRDEQYGASELVMQAELAMVQSRAAGRNVFRFFD 459

Query: 58  PAMQTVVLERAALEAGLRKAIDDGQLVLHYQAQVVEGGRVTGAEVLVRWQH 108
           PAMQ +  +R+ LEA LR+A+   Q +++YQ QV   G V GAE LVRWQH
Sbjct: 460 PAMQALANQRSQLEAELRQAVARRQFIVYYQPQVTYEGDVVGAEALVRWQH 510


>gi|300312904|ref|YP_003776996.1| diguanylate
           cyclase/phosphodiesterase with PAS/PAC sensor domains
           protein [Herbaspirillum seropedicae SmR1]
          Length = 701

 Score = 88.6 bits (218), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/104 (40%), Positives = 66/104 (63%), Gaps = 1/104 (0%)

Query: 5   PYQLGEVEYRTTASVGATVFRGRQASIDELLKQADLAMYKSKETGRNAISFFDPAMQTVV 64
           P+Q G+ E++ TAS+G + +      ++ LLK AD AMY++KE GRN   FF P M + V
Sbjct: 377 PWQAGDREFQVTASIGVSRYPADGKDVESLLKHADSAMYRAKEQGRNNFQFFAPWMDSQV 436

Query: 65  LERAALEAGLRKAIDDGQLVLHYQAQV-VEGGRVTGAEVLVRWQ 107
             R  +   LR+A+D  +  L+YQ ++ ++ GR+ GAE L+RW+
Sbjct: 437 SNRLEMLINLRRALDQDEFKLYYQPKLSLQDGRLIGAEALIRWE 480


>gi|300312026|ref|YP_003776118.1| signal transduction protein
           containing a membrane domain, an EAL and a GGDEF
           domain-containing protein [Herbaspirillum seropedicae
           SmR1]
          Length = 1106

 Score = 87.8 bits (216), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 47/125 (37%), Positives = 68/125 (54%), Gaps = 18/125 (14%)

Query: 2   LDSPYQLGEV-----------------EYRTTASVGATVFRGRQASIDELLKQADLAMYK 44
            D P QLGE+                 E   + S+G   + G   +   L+K AD+AMY+
Sbjct: 760 FDDPVQLGEIAQKLLTEARKPFIIDGQEAMLSVSIGIATYPGDGDNAQTLIKNADIAMYR 819

Query: 45  SKETGRNAISFFDPAMQTVVLERAALEAGLRKAIDDGQLVLHYQAQV-VEGGRVTGAEVL 103
           +K  G++   FF   + T  +ER ALEA LR+AI+  + V+HYQ ++ +  GR+ GAE L
Sbjct: 820 AKHHGKDDYRFFSDEINTNTVERIALEAELRRAIERAEFVVHYQPKIELAEGRIVGAEAL 879

Query: 104 VRWQH 108
           VRWQH
Sbjct: 880 VRWQH 884


  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    0.384 

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: 352,416
Number of extensions: 12135
Number of successful extensions: 98
Number of sequences better than 1.0e-08: 11
Number of HSP's gapped: 91
Number of HSP's successfully gapped: 11
Length of query: 121
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 47
Effective length of database: 1,269,480
Effective search space: 59665560
Effective search space used: 59665560
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: 125 (52.8 bits)