BLASTP 2.2.17 [Aug-26-2007]

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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= 0001.0162.p         (117 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects 
           15,459,386 sequences; 5,307,515,862 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|YP_003773760.1| HU histone family DNA-binding protein [Herba...   178   3e-43
ref|YP_004750762.1| histone family protein DNA-binding protein [...   119   1e-25
ref|YP_001156801.1| histone family protein DNA-binding protein [...   115   3e-24
ref|YP_001798416.1| histone family protein DNA-binding protein [...   115   3e-24
ref|ZP_08273299.1| DNA-binding protein HU [Oxalobacteraceae bact...   114   4e-24

>ref|YP_003773760.1| HU histone family DNA-binding protein [Herbaspirillum seropedicae
           SmR1]
 gb|ADJ61852.1| HU histone family DNA-binding protein [Herbaspirillum seropedicae
           SmR1]
          Length = 115

 Score =  178 bits (451), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 113/115 (98%), Positives = 115/115 (100%)

Query: 3   LRIRLIPVLKSGHLNSERNFKVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG 62
           +RIRLIPVLKSGHLNSERNF+VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG
Sbjct: 1   MRIRLIPVLKSGHLNSERNFQVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKG 60

Query: 63  DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 117
           DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK
Sbjct: 61  DTVQLVGFGSFSTGKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 115


>ref|YP_004750762.1| histone family protein DNA-binding protein [Collimonas fungivorans
           Ter331]
 gb|AEK59939.1| histone family protein DNA-binding protein [Collimonas fungivorans
           Ter331]
          Length = 94

 Score =  119 bits (299), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 76/94 (80%), Positives = 88/94 (93%)

Query: 24  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 83
           +NK+EL+D IA D EISKAAAQRAL+SV++N+IKAVTKG TVQL+GFGSFS+GKRAARTG
Sbjct: 1   MNKTELIDAIATDCEISKAAAQRALESVVDNVIKAVTKGSTVQLIGFGSFSSGKRAARTG 60

Query: 84  RNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 117
           RNP+TGE IKIAAA TVKF+AGKAFK+AVNKKKK
Sbjct: 61  RNPRTGEAIKIAAAKTVKFTAGKAFKDAVNKKKK 94


>ref|YP_001156801.1| histone family protein DNA-binding protein [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gb|ABP35237.1| HU family DNA-binding protein [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
          Length = 106

 Score =  115 bits (287), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 68/102 (66%), Positives = 86/102 (84%)

Query: 16  LNSERNFKVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFST 75
           +N  +   +NK+EL+  IA D EISKA A+ AL+S I+ IIKAVTKGD+VQL+GFG+F++
Sbjct: 5   INIYKELHLNKAELIAAIADDAEISKAKAEFALNSAIDTIIKAVTKGDSVQLIGFGTFAS 64

Query: 76  GKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 117
           GKRAAR GRNP+TGE +KIAAA TVKFSAGKAFK++VNK+KK
Sbjct: 65  GKRAARMGRNPKTGEPLKIAAAKTVKFSAGKAFKDSVNKRKK 106


>ref|YP_001798416.1| histone family protein DNA-binding protein [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gb|ACB44802.1| histone family protein DNA-binding protein [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 106

 Score =  115 bits (287), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 69/102 (67%), Positives = 86/102 (84%)

Query: 16  LNSERNFKVNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFST 75
           +N  +   +NK+EL+  IA D EISKA A+ AL+S IENIIKAVTKGD+VQL+GFG+F++
Sbjct: 5   INIYKELHLNKAELIAAIADDAEISKAKAEFALNSAIENIIKAVTKGDSVQLIGFGTFAS 64

Query: 76  GKRAARTGRNPQTGEEIKIAAATTVKFSAGKAFKEAVNKKKK 117
            KRAAR GRNP+TGE +KIAAA TVKFSAGKAFK++VNK+KK
Sbjct: 65  SKRAARMGRNPKTGEPLKIAAAKTVKFSAGKAFKDSVNKRKK 106


>ref|ZP_08273299.1| DNA-binding protein HU [Oxalobacteraceae bacterium IMCC9480]
 gb|EGF33226.1| DNA-binding protein HU [Oxalobacteraceae bacterium IMCC9480]
          Length = 91

 Score =  114 bits (286), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 63/91 (69%), Positives = 80/91 (87%)

Query: 24  VNKSELVDVIAADTEISKAAAQRALDSVIENIIKAVTKGDTVQLVGFGSFSTGKRAARTG 83
           +NK+EL+D IAAD ++ K  AQRAL+S++ N+I+AV  GD+VQL+GFG+F++G RA RTG
Sbjct: 1   MNKTELIDAIAADCDLPKTVAQRALESILSNVIQAVVNGDSVQLIGFGAFASGSRAERTG 60

Query: 84  RNPQTGEEIKIAAATTVKFSAGKAFKEAVNK 114
           RNP+TGEEIKIAAA TVKFSAGKAFK+AVNK
Sbjct: 61  RNPRTGEEIKIAAAKTVKFSAGKAFKDAVNK 91