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= 0504.0025.p
         (83 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|ZP_00097478.1| COG1695: Predicted transcriptional regulators...   108   4e-23
ref|ZP_00060436.1| COG1695: Predicted transcriptional regulators...    66   2e-10
ref|NP_489012.1| hypothetical protein [Nostoc sp. PCC 7120] >gi|...    61   1e-08
ref|NP_767796.1| transcriptional regulatory protein [Bradyrhizob...    59   5e-08
ref|ZP_00108653.1| COG1695: Predicted transcriptional regulators...    59   5e-08

>ref|ZP_00097478.1| COG1695: Predicted transcriptional regulators [Desulfitobacterium
          hafniense]
          Length = 177

 Score =  108 bits (270), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/74 (64%), Positives = 60/74 (81%)

Query: 2  TGYDLKKLIQESSFLYWSGNNNQIYKALVELLNAGFVTNEVRHQDSSPSKKIYTITSSGL 61
          TGY+LKK+ +ESSF+YWSGNNNQIYKAL+++     VTNEV HQ+SSPSKK+YTIT  GL
Sbjct: 26 TGYELKKIFEESSFMYWSGNNNQIYKALIKMQEEELVTNEVIHQESSPSKKVYTITEEGL 85

Query: 62 AELRKWVVAPPEPP 75
           +L+ WV+  PE P
Sbjct: 86 KKLKTWVLHSPEVP 99


>ref|ZP_00060436.1| COG1695: Predicted transcriptional regulators [Clostridium
          thermocellum ATCC 27405]
          Length = 195

 Score = 66.2 bits (160), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 45/68 (66%)

Query: 1  MTGYDLKKLIQESSFLYWSGNNNQIYKALVELLNAGFVTNEVRHQDSSPSKKIYTITSSG 60
          MTGY++ K+ ++S   +W+ N +QIY+ L  L   GFVT+ V  Q   P KK+++IT SG
Sbjct: 30 MTGYEIMKVFRDSLSFFWTANTSQIYRELNTLKKDGFVTDIVVKQTGKPDKKVFSITESG 89

Query: 61 LAELRKWV 68
            EL++W+
Sbjct: 90 REELKRWL 97


>ref|NP_489012.1| hypothetical protein [Nostoc sp. PCC 7120]
 pir||AD2427 hypothetical protein all4972 [imported] - Nostoc sp. (strain PCC
          7120)
 dbj|BAB76671.1| ORF_ID:all4972~hypothetical protein [Nostoc sp. PCC 7120]
          Length = 179

 Score = 60.8 bits (146), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 44/73 (60%)

Query: 2  TGYDLKKLIQESSFLYWSGNNNQIYKALVELLNAGFVTNEVRHQDSSPSKKIYTITSSGL 61
          +GYDL K+  ES   +W  +  QIY+ L +L +AG + +EV  ++    KK+Y+IT  G 
Sbjct: 17 SGYDLSKVFSESVGYFWQASQQQIYRELGKLESAGLIVSEVIPREGRLDKKVYSITEQGK 76

Query: 62 AELRKWVVAPPEP 74
           +L +W+  P EP
Sbjct: 77 QQLIEWMHKPSEP 89


>ref|NP_767796.1| transcriptional regulatory protein [Bradyrhizobium japonicum]
 dbj|BAC46421.1| transcriptional regulatory protein [Bradyrhizobium japonicum USDA
          110]
          Length = 196

 Score = 58.5 bits (140), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 38/74 (51%)

Query: 1  MTGYDLKKLIQESSFLYWSGNNNQIYKALVELLNAGFVTNEVRHQDSSPSKKIYTITSSG 60
          MTGY+L K    S   +W  ++ QIY+ L +L + G++      Q   P+K +YT+T  G
Sbjct: 16 MTGYELAKTFDSSIGFFWKADHQQIYRELSKLRDRGYIQGREVVQTGKPNKLVYTLTPEG 75

Query: 61 LAELRKWVVAPPEP 74
             LR W   P  P
Sbjct: 76 RTALRHWAARPSTP 89


>ref|ZP_00108653.1| COG1695: Predicted transcriptional regulators [Nostoc
          punctiforme]
          Length = 182

 Score = 58.5 bits (140), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 1  MTGYDLKKLIQESSFLYWSGNNNQIYKALVELLNAGFVTNEVRHQDSSPSKKIYTITSSG 60
           +GYDL K    S   +WS ++ QIY+ L +L +  ++++E   Q   P K++Y++T  G
Sbjct: 16 CSGYDLAKRFDGSVGFFWSASHQQIYRELSKLEDQEWISSETILQAGRPDKRLYSVTDLG 75

Query: 61 LAELRKWVVAPPEP 74
             L++W+  P EP
Sbjct: 76 QQHLKEWIAQPCEP 89


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
Lambda     K      H
   0.315    0.132    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 2715099
Number of Hits to DB: 127,282,360
Number of extensions: 4121640
Number of successful extensions: 12515
Number of sequences better than 1.0e-05: 22
Number of HSP's gapped: 12520
Number of HSP's successfully gapped: 22
Length of query: 83
Length of database: 757,237,578
Length adjustment: 52
Effective length of query: 31
Effective length of database: 616,052,430
Effective search space: 19097625330
Effective search space used: 19097625330
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 (21.5 bits)
S2: 120 (50.8 bits)