RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780476|ref|YP_003064889.1| two component response
regulator [Candidatus Liberibacter asiaticus str. psy62]
         (123 letters)



>1mb3_A Cell division response regulator DIVK; signal transduction protein,
           structural proteomics in europe, spine, structural
           genomics; 1.41A {Caulobacter vibrioides} SCOP: c.23.1.1
           PDB: 1m5u_A 1mav_A 1mb0_A 1m5t_A
          Length = 124

 Score =  120 bits (303), Expect = 8e-29
 Identities = 85/118 (72%), Positives = 102/118 (86%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           KKV+IVEDNELNMKLF DL+E  GY  LQTR G+ AL +AR++KPD+I+MDIQL EISGL
Sbjct: 2   KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENKPDLILMDIQLPEISGL 61

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           E+TK +KED +L  IPV+AVTAFAMKGDEERIR+GGCEAYISKPIS+  F+ETIK+ +
Sbjct: 62  EVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLL 119


>1w25_A Stalked-cell differentiation controlling protein; two-component
           system, response regulator, diguanylate cyclase, ggdef
           domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP:
           c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A*
          Length = 459

 Score =  111 bits (279), Expect = 4e-26
 Identities = 28/117 (23%), Positives = 62/117 (52%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           ++++V+D E N++L    +    Y      +G  AL +A +  PD+I++D+ +  + G  
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFT 62

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + +++K+D   + IPV+ +TA   +GD  +  + G   +++KPI   +    ++   
Sbjct: 63  VCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLT 119



 Score = 56.3 bits (135), Expect = 2e-09
 Identities = 20/105 (19%), Positives = 48/105 (45%), Gaps = 2/105 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            +V+IV+DNE   +     +       +   +  E  +++     D++I++   +   GL
Sbjct: 153 GRVLIVDDNERQAQRVAAELGVEHRPVI--ESDPEKAKISAGGPVDLVIVNAAAKNFDGL 210

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPI 107
             T  ++ +   +++PV+A+     +G   +  + G    +S+PI
Sbjct: 211 RFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPI 255


>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase,
           lyase-transferase COMP; 2.50A {Xanthomonas campestris
           PV}
          Length = 143

 Score =  105 bits (264), Expect = 3e-24
 Identities = 24/117 (20%), Positives = 62/117 (52%), Gaps = 2/117 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           ++++ +D+E N  + + L+E +G+  L      + L+   +   D +I+D+ +  ++GL+
Sbjct: 16  RMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLD 75

Query: 64  ITKQIKE--DSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           + KQ++    S ++  PV+ ++A           + G  A+++KP+  +  ++T+  
Sbjct: 76  MLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLAD 132


>3nhm_A Response regulator; protein structure initiative II(PSI II),
           NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}
          Length = 133

 Score =  105 bits (263), Expect = 3e-24
 Identities = 28/120 (23%), Positives = 57/120 (47%), Gaps = 2/120 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           +  KV+IVE++    +  R L+    +      +G   L+ A  H PDV+I D+ +  + 
Sbjct: 3   LKPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQALAHPPDVLISDVNMDGMD 61

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G  +    + +  L+ IPVI V+ +A + +    +    +AY+ KP+   + +  +   +
Sbjct: 62  GYALCGHFRSEPTLKHIPVIFVSGYAPRTEGPADQ-PVPDAYLVKPVKPPVLIAQLHALL 120


>3lte_A Response regulator; structural genomics, PSI, protein structure
           initiative, nysgrc, NEW YORK structural genomix research
           consortium; 2.00A {Bermanella marisrubri}
          Length = 132

 Score =  102 bits (257), Expect = 2e-23
 Identities = 20/120 (16%), Positives = 57/120 (47%), Gaps = 1/120 (0%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           K++++V+D++        +++   +      NG +A       +P ++ +D+ + ++ GL
Sbjct: 7   KRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGL 66

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGE 122
           ++ + ++++ ++   P I V +   K   ++    G + Y+ KP      ++ I   + E
Sbjct: 67  DVIRSLRQN-KVANQPKILVVSGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLVNE 125


>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver
           domain, cytoplasm, DNA-binding, phosphoprotein,
           transcription regulation; 1.95A {Bacillus subtilis} PDB:
           2zwm_A
          Length = 120

 Score =  102 bits (256), Expect = 2e-23
 Identities = 30/118 (25%), Positives = 64/118 (54%), Gaps = 3/118 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M KK+++V+D +    +    +   GY      +G EA+E+  + +PD+I++DI L    
Sbjct: 1   MDKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKD 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           G+E+ +++++     ++P+I +TA   + D+    + G + Y++KP S    +  +K 
Sbjct: 61  GVEVCREVRKKY---DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKA 115


>3eq2_A Probable two-component response regulator; adaptor sigmas,
           signaling protein; 3.40A {Pseudomonas aeruginosa}
          Length = 394

 Score =  100 bits (251), Expect = 8e-23
 Identities = 28/122 (22%), Positives = 65/122 (53%), Gaps = 2/122 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           +   ++I++D+E+  +     +E S +  LQ  NG++ L++    +PD++I D+++ +I 
Sbjct: 4   VSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQPDLVICDLRMPQID 63

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           GLE+ ++I++ +   E P+I ++   +  D     + G   Y+ KP+     +E   +  
Sbjct: 64  GLELIRRIRQTA--SETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRA 121

Query: 121 GE 122
            +
Sbjct: 122 LD 123


>3i42_A Response regulator receiver domain protein (CHEY- like); structural
           genomics, PSI-2, protein structure initiative; 2.15A
           {Methylobacillus flagellatus KT}
          Length = 127

 Score =  100 bits (251), Expect = 8e-23
 Identities = 31/120 (25%), Positives = 59/120 (49%), Gaps = 1/120 (0%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           L++ +IVED +   + F++L+E  G+ A    +G +AL        D + +D+ L + SG
Sbjct: 3   LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSG 62

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIG 121
           L + KQ++     +    +AV+ FA   D  +      + Y+ KPI ++     ++   G
Sbjct: 63  LALVKQLRALPMEKTSKFVAVSGFAK-NDLGKEACELFDFYLEKPIDIASLEPILQSIEG 121


>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia
           coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A
           1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A
           1djm_A 1kmi_Y* 1d4z_A 1cye_A 2che_A 2chf_A 2pl9_A*
           2pmc_A ...
          Length = 128

 Score =  100 bits (250), Expect = 9e-23
 Identities = 29/118 (24%), Positives = 58/118 (49%), Gaps = 1/118 (0%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKPDVIIMDIQLQEISGL 62
           K ++V+D     ++ R+L++  G+  ++   +G++AL   +      +I D  +  + GL
Sbjct: 6   KFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGL 65

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           E+ K I+    +  +PV+ VTA A K +     + G   Y+ KP + +   E + K  
Sbjct: 66  ELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIF 123


>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm,
           flagellar rotatio magnesium, metal-binding,
           phosphoprotein; 1.70A {Helicobacter pylori} PDB: 3gwg_A
           3h1e_A 3h1f_A
          Length = 129

 Score = 99.7 bits (249), Expect = 2e-22
 Identities = 35/121 (28%), Positives = 66/121 (54%), Gaps = 2/121 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGY-IALQTRNGMEALE-LARQHKPDVIIMDIQLQEIS 60
            K+++V+D+    ++ ++ +   GY   L+  +G+EA E L       V+I D  + E++
Sbjct: 6   MKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTKVLITDWNMPEMN 65

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           GL++ K+++ DS  +EIP+I +TA   K +     K G   YI KP +  +  E ++  +
Sbjct: 66  GLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL 125

Query: 121 G 121
           G
Sbjct: 126 G 126


>3kht_A Response regulator; PSI-II, structural genomics, protein structure
           initiative, NEW YORK SGX research center for structural
           genomics; 2.10A {Hahella chejuensis kctc 2396}
          Length = 144

 Score = 96.9 bits (241), Expect = 1e-21
 Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 3/118 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           K+V++VEDN  ++ L R +++            NG +AL   +Q K D+II+DI L   +
Sbjct: 6   KRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIAN 65

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPI-SLSIFMETIK 117
           G E+   +++    Q  P++ +T        ++    G  + + K   +++ F   I 
Sbjct: 66  GFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIY 123


>3bre_A Probable two-component response regulator; protein-nucleotide
           complex, signaling protein; HET: C2E; 2.40A {Pseudomonas
           aeruginosa PAO1} PDB: 3i5a_A*
          Length = 358

 Score = 96.7 bits (240), Expect = 1e-21
 Identities = 22/118 (18%), Positives = 51/118 (43%), Gaps = 1/118 (0%)

Query: 4   KVMIVEDNELNMKLFRDLIET-SGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            V++V+D  +  +  R  + + +G       +  +A+ +A Q KP VI+ D+ +  + GL
Sbjct: 20  MVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGL 79

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
            +    + +   ++IP+I ++       +      G   Y+ K       +  I+ + 
Sbjct: 80  TLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHS 137


>2ayx_A Sensor kinase protein RCSC; two independent structural domains,
           transferase; NMR {Escherichia coli} SCOP: c.23.1.1
           c.23.1.6 PDB: 2ayz_A 2ayy_A
          Length = 254

 Score = 96.7 bits (240), Expect = 1e-21
 Identities = 30/117 (25%), Positives = 70/117 (59%), Gaps = 2/117 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            +++V+D+ +N +L  D + + GY      +G++AL +  ++  D+++ D+ +  + G  
Sbjct: 131 MILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYR 190

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           +T++I++      +PVI VTA A+  +++R  + G ++ +SKP++L +  +T+  Y 
Sbjct: 191 LTQRIRQLG--LTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYA 245



 Score = 25.4 bits (55), Expect = 3.7
 Identities = 9/66 (13%), Positives = 18/66 (27%), Gaps = 7/66 (10%)

Query: 3  KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
          K+  +   N    +     ++ SG         +   E       DV+I D  + +    
Sbjct: 12 KRCWLAVRNASLCQFLETSLQRSGI-------VVTTYEGQEPTPEDVLITDEVVSKKWQG 64

Query: 63 EITKQI 68
                
Sbjct: 65 RAVVTF 70


>2zwm_A Transcriptional regulatory protein YYCF; two-component system,
           response regulator, dimerization domain, phosphorylation
           site, cytoplasm; 2.04A {Bacillus subtilis}
          Length = 130

 Score = 96.1 bits (239), Expect = 2e-21
 Identities = 30/120 (25%), Positives = 65/120 (54%), Gaps = 3/120 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M KK+++V+D +    +    +   GY      +G EA+E+  + +PD+I++DI L    
Sbjct: 1   MDKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKD 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G+E+ +++++     ++P+I +TA   + D+    + G + Y++KP S    +  +K  +
Sbjct: 61  GVEVCREVRKKY---DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANL 117


>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer,
           APO-protein, (beta/alpha)5, signaling protein; 1.75A
           {Tolypothrix SP} SCOP: c.23.1.1
          Length = 149

 Score = 96.2 bits (239), Expect = 2e-21
 Identities = 34/130 (26%), Positives = 67/130 (51%), Gaps = 12/130 (9%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIA--LQTRNGMEALELARQH----------KPDVI 50
           + +++VED++ +   F+ L++  G +    +   G +AL+   Q           +P VI
Sbjct: 7   QPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVI 66

Query: 51  IMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLS 110
           ++D+ L    G E+ ++IK+D  L++IPV+ +T  +   D E        +YI KP+ + 
Sbjct: 67  LLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID 126

Query: 111 IFMETIKKYI 120
              ET++ +I
Sbjct: 127 RLTETVQTFI 136


>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY
           homologue, homodimer, (beta/alpha)5, signaling protein;
           HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1
          Length = 140

 Score = 95.4 bits (237), Expect = 3e-21
 Identities = 35/125 (28%), Positives = 65/125 (52%), Gaps = 9/125 (7%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQ-------HKPDVIIMD 53
           KK+ +VEDN+ +++L ++ +  S   +  +  R+GMEA+   RQ        +PD+I++ 
Sbjct: 3   KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLX 62

Query: 54  IQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFM 113
           + L +  G E+  +IK D  L+ IPV+ ++    + D           YI+K  +LS   
Sbjct: 63  LNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLF 122

Query: 114 ETIKK 118
           + +K 
Sbjct: 123 QIVKG 127


>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein
           structure initiative; 2.04A {Staphylococcus aureus}
          Length = 133

 Score = 94.5 bits (235), Expect = 6e-21
 Identities = 37/119 (31%), Positives = 65/119 (54%), Gaps = 4/119 (3%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEI 59
           L  ++I ED  +  +    LI+  G   +   T NG++A++L  ++ P+V+I+DI++  +
Sbjct: 3   LTSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIEEYNPNVVILDIEMPGM 62

Query: 60  SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           +GLE+  +I++      I VI VT F   G  E+      +AY+ K  S+   +ETI K
Sbjct: 63  TGLEVLAEIRKKH--LNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINK 119


>3lua_A Response regulator receiver protein; two-component signal
           transduction system, histidine kinase, phosphorelay,
           receiver domain, nysgxrc; 2.40A {Clostridium
           thermocellum}
          Length = 140

 Score = 93.5 bits (233), Expect = 1e-20
 Identities = 26/123 (21%), Positives = 48/123 (39%), Gaps = 3/123 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSG-YIALQTRNGMEALELARQH-KPDVIIMDIQL-Q 57
           +   V++++  E   +  + + +  G Y  ++  N  +   + +      +IIMDI    
Sbjct: 3   LDGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPV 62

Query: 58  EISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
           E  GLE+   I+ +S     PVI  T     G      K     YI KP        +++
Sbjct: 63  EKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVR 122

Query: 118 KYI 120
             +
Sbjct: 123 SVL 125


>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket,
           two component system; 1.90A {Bacillus subtilis} SCOP:
           c.23.1.1 PDB: 1pey_A 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A
           2jvj_A 2jvk_A 2jvi_A 1f51_E
          Length = 124

 Score = 93.4 bits (232), Expect = 1e-20
 Identities = 33/120 (27%), Positives = 67/120 (55%), Gaps = 2/120 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M +K++IV+D      L  ++    GY   Q  NG++AL++  + +PD++++D+++  + 
Sbjct: 2   MNEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMD 61

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G+EI K++K   E   I VI +TA+      +  ++ G   + +KP  +    + +KKY+
Sbjct: 62  GIEILKRMKVIDE--NIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 119


>1p6q_A CHEY2; chemotaxis, signal transduction, response regulator,
           structural proteomics in europe, spine, structural
           genomics; NMR {Sinorhizobium meliloti} SCOP: c.23.1.1
           PDB: 1p6u_A
          Length = 129

 Score = 93.4 bits (232), Expect = 1e-20
 Identities = 22/119 (18%), Positives = 56/119 (47%), Gaps = 1/119 (0%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKPDVIIMDIQLQEISGL 62
           KV+IV+D   +  L  D ++  G+  +    +G + +++  Q+   ++I D  + ++ GL
Sbjct: 8   KVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGL 67

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIG 121
            + + ++ +   ++   I +TA   +   ++    G    ++KP ++      I+   G
Sbjct: 68  GLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFG 126


>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A
           {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A
          Length = 149

 Score = 92.8 bits (230), Expect = 2e-20
 Identities = 28/125 (22%), Positives = 69/125 (55%), Gaps = 9/125 (7%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQH-------KPDVIIMD 53
           K +++VED++ + +L +++++TS   +  +  R+G+ A+   +Q        +P++I++D
Sbjct: 9   KVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLD 68

Query: 54  IQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFM 113
           + L +  G E+  +IK++ +L+ IPV+ +T    + D     +     Y++K  +L    
Sbjct: 69  LNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLF 128

Query: 114 ETIKK 118
           + ++ 
Sbjct: 129 KMVQG 133


>3f6c_A Positive transcription regulator EVGA; structural genomics, ,
           PSI-2, protein structure initiative; 1.45A {Escherichia
           coli k-12}
          Length = 134

 Score = 92.1 bits (229), Expect = 3e-20
 Identities = 21/116 (18%), Positives = 55/116 (47%), Gaps = 3/116 (2%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGY-IALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             +I++D+ L +   R+L+  +   I  +   G  A++     KPD++I+D+ +  ++G+
Sbjct: 3   NAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGI 62

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           ++ + +++        +I V+A       +     G   ++SK   ++  +  I+ 
Sbjct: 63  QVLETLRKRQ--YSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEA 116


>3hdg_A Uncharacterized protein; two-component sensor activity, response
           regulator, PSI-II, 11227F, NYSGXRC, structural genomics;
           2.27A {Wolinella succinogenes}
          Length = 137

 Score = 92.2 bits (229), Expect = 3e-20
 Identities = 33/116 (28%), Positives = 56/116 (48%), Gaps = 2/116 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           K++IVED+    +    +I           +G E   L   H PDVII DI++ ++ GLE
Sbjct: 9   KILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLE 68

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
           +  +IK      +  VI ++AF+      +  + G   ++ KPI     MET++ +
Sbjct: 69  MLDRIKAGG--AKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDF 122


>1mvo_A PHOP response regulator; phosphate regulon, transcriptional
           regulatory protein, alpha/beta doubly wound fold,
           phosphorylation; 1.60A {Bacillus subtilis} SCOP:
           c.23.1.1
          Length = 136

 Score = 91.9 bits (228), Expect = 3e-20
 Identities = 36/120 (30%), Positives = 68/120 (56%), Gaps = 2/120 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M KK+++V+D E  + L +  +E SGY  +   +G EAL+ A   KPD+I++D+ L ++ 
Sbjct: 2   MNKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLD 61

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G+E+ KQ+++       P++ +TA   + D+    + G + Y++KP S       +K  +
Sbjct: 62  GIEVCKQLRQQK--LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAIL 119


>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping;
           1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB:
           1qmp_A*
          Length = 130

 Score = 91.1 bits (226), Expect = 5e-20
 Identities = 31/125 (24%), Positives = 61/125 (48%), Gaps = 3/125 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQE 58
           M  KV I +DN   + L  + I +     +     NG + L++  + +PD++++DI +  
Sbjct: 1   MSIKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPH 60

Query: 59  ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           + GL + ++I+   E Q   VI +TAF  +   ++  + G   +I KP  +      I++
Sbjct: 61  LDGLAVLERIRAGFEHQ-PNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQ 119

Query: 119 YIGEA 123
             G+ 
Sbjct: 120 VYGKT 124


>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH
           sides, signaling protein; HET: BFD; 1.80A {Thermotoga
           maritima} PDB: 3dgf_C 3dge_C
          Length = 122

 Score = 89.7 bits (222), Expect = 1e-19
 Identities = 39/122 (31%), Positives = 66/122 (54%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M KKV++V+D+ +  K+    ++  GY  ++  NG  ALE   +  PD+I++ I +  + 
Sbjct: 1   MSKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMD 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G  + K+++E  E + IPVI +TA   + DE      G    + KP S S F+E +K  +
Sbjct: 61  GFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL 120

Query: 121 GE 122
            E
Sbjct: 121 NE 122


>3cnb_A DNA-binding response regulator, MERR family; signal receiver
           domain, DNA binding protein, protein structure
           initiative, PSI-2; 2.00A {Colwellia psychrerythraea 34H}
          Length = 143

 Score = 88.5 bits (219), Expect = 4e-19
 Identities = 30/119 (25%), Positives = 55/119 (46%), Gaps = 2/119 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIET--SGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
            ++I+ED++    +    +E            N  +A +L    KPDV+++D+ +  + G
Sbjct: 10  SILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDG 69

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
             I  +IK       I VIA+T      +  RI   G E    KP++ ++  +TIK+ +
Sbjct: 70  FSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLV 128


>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein
           interaction, histidine kinase, response regulator,
           phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB:
           3kyi_B*
          Length = 145

 Score = 88.4 bits (219), Expect = 4e-19
 Identities = 30/108 (27%), Positives = 53/108 (49%), Gaps = 4/108 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALE-LARQHKPDVIIMDIQLQEIS 60
            VMIV+D  +        I+T     +  Q  NG EAL+ LA Q   D+I++DI++  + 
Sbjct: 15  NVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMD 74

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPIS 108
           G+E  +  K  +  + I +++  A +      R R+ G +  ++KP  
Sbjct: 75  GMEFLRHAKLKTRAK-ICMLSSVAVSGSPHAARARELGADGVVAKPSG 121


>3eul_A Possible nitrate/nitrite response transcriptional regulatory
           protein NARL (DNA-binding...; central beta strand
           flanked by alpha helices; 1.90A {Mycobacterium
           tuberculosis}
          Length = 152

 Score = 87.6 bits (217), Expect = 7e-19
 Identities = 20/117 (17%), Positives = 53/117 (45%), Gaps = 4/117 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           +V++ +D+ L  +     +  SG + +  +  +G  ALEL + H PDV ++D ++  + G
Sbjct: 17  RVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDG 76

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
            ++   ++         V+ ++A        +  + G   ++ K  + +  ++ +  
Sbjct: 77  AQVAAAVRSYE--LPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLD 131


>3c97_A Signal transduction histidine kinase; structural genomics,
           signaling, PSI-2, protein structure initiative; 1.70A
           {Aspergillus oryzae RIB40}
          Length = 140

 Score = 87.3 bits (216), Expect = 7e-19
 Identities = 29/123 (23%), Positives = 54/123 (43%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M   V+I EDN++   +    +E          NG++AL+  +  + DVIIMDIQ+  + 
Sbjct: 9   MPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQFDVIIMDIQMPVMD 68

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           GLE   +I+           ++ A      ++       + Y+SKP++ +   + +    
Sbjct: 69  GLEAVSEIRNYERTHNTKRASIIAITADTIDDDRPGAELDEYVSKPLNPNQLRDVVLTCH 128

Query: 121 GEA 123
            E 
Sbjct: 129 SEG 131


>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural
           genomics, protein structure initiative; 1.50A
           {Pseudomonas fluorescens pf-5}
          Length = 153

 Score = 87.3 bits (216), Expect = 8e-19
 Identities = 21/119 (17%), Positives = 51/119 (42%), Gaps = 3/119 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            ++++V+  E+ ++  + L+    Y     R+  +AL+L    + D++I    L ++ G 
Sbjct: 15  PEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASREVDLVISAAHLPQMDGP 74

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEER-IRKGGCEAYISKPISLSIFMETIKKYI 120
            +  +I +         I +T         + I +G    Y+SKP      +  +++ +
Sbjct: 75  TLLARIHQQY--PSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQAL 131


>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal
           transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1
           PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y
          Length = 120

 Score = 86.9 bits (215), Expect = 1e-18
 Identities = 36/119 (30%), Positives = 64/119 (53%), Gaps = 3/119 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGY-IALQTRNGMEALELARQHKPDVIIMDIQLQEI 59
           M K+V+IV+D      + +D+I  +GY +A +  NG EA+E  ++ KPD++ MDI + E+
Sbjct: 1   MGKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEM 60

Query: 60  SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           +G++  K+I +        +I  +A   +       K G + +I KP   S  +E + K
Sbjct: 61  NGIDAIKEIMKID--PNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNK 117


>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II),
           NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas
           SP}
          Length = 140

 Score = 86.2 bits (213), Expect = 2e-18
 Identities = 23/119 (19%), Positives = 61/119 (51%), Gaps = 1/119 (0%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            +++I ED+    +L   ++E  G+ +    +  +ALE   +     + +D+ L +  G+
Sbjct: 7   PRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGV 66

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGD-EERIRKGGCEAYISKPISLSIFMETIKKYI 120
            + + ++ DS  +++ ++ V+A A +G+ E   +      ++ KPI  ++ + ++ + I
Sbjct: 67  SLIRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAI 125


>1s8n_A Putative antiterminator; structural genomics, transcriptional
           antiterminator, two component system, PSI; 1.48A
           {Mycobacterium tuberculosis H37RV} SCOP: c.23.1.1 PDB:
           1sd5_A
          Length = 205

 Score = 86.1 bits (212), Expect = 2e-18
 Identities = 37/119 (31%), Positives = 64/119 (53%), Gaps = 4/119 (3%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKPDVIIMDIQLQEISG 61
           ++V+I ED  L      +++   GY  +    +G EA+ELA  HKPD++IMD+++    G
Sbjct: 14  RRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDG 73

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           ++   +I         P++ +TAF+ +   ER R  G  AY+ KP S+S  +  I+  +
Sbjct: 74  IDAASEIASKR---IAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAV 129


>1dcf_A ETR1 protein; beta-alpha five sandwich; 2.50A {Arabidopsis
           thaliana} SCOP: c.23.1.2
          Length = 136

 Score = 85.8 bits (212), Expect = 2e-18
 Identities = 23/121 (19%), Positives = 53/121 (43%), Gaps = 4/121 (3%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            KV+++++N ++  + + L+   G       +  E L     H+  V+ MD+ +  +   
Sbjct: 8   LKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLR-VVSHEHKVVFMDVCMPGVENY 66

Query: 63  EITKQIKE---DSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
           +I  +I E       Q   ++A++    K  +E+    G +  + KP+SL    + +   
Sbjct: 67  QIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDL 126

Query: 120 I 120
           +
Sbjct: 127 L 127


>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory
           protein; receiver domain, 2-component signal
           transduction; 1.7A {Sinorhizobium meliloti} SCOP:
           c.23.1.1 PDB: 1l5z_A 1l5y_A
          Length = 155

 Score = 85.8 bits (212), Expect = 3e-18
 Identities = 22/117 (18%), Positives = 52/117 (44%), Gaps = 2/117 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            V +++D+    K  +  +E +G+      +  EAL         ++I DI++  + GL 
Sbjct: 5   SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLA 64

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + ++I       ++P+I VT         +  + G   +I+KP +    +++ ++  
Sbjct: 65  LFRKILALD--PDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAE 119


>2jba_A Phosphate regulon transcriptional regulatory protein PHOB;
           transcription factor, sensory transduction, phosphate
           regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A
           2iyn_A 2jb9_A 1zes_A
          Length = 127

 Score = 85.4 bits (211), Expect = 3e-18
 Identities = 29/120 (24%), Positives = 63/120 (52%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M +++++VED     ++   ++E +G+  ++  +   A+    +  PD+I++   L   S
Sbjct: 1   MARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGS 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G++  K ++ +S  ++IPV+ +TA   + D  R  + G +  I+KP S    +  IK  +
Sbjct: 61  GIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVM 120


>1dc7_A NTRC, nitrogen regulation protein; receiver domain,
           phosphorylation, signal transduction, conformational
           rearrangement; NMR {Salmonella typhimurium} SCOP:
           c.23.1.1 PDB: 1j56_A 1krw_A 1krx_A 1ntr_A 1dc8_A*
          Length = 124

 Score = 85.4 bits (211), Expect = 3e-18
 Identities = 29/118 (24%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             V +V+D+     +    +  +G       NG E L       PDV++ DI++  + GL
Sbjct: 4   GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPGMDGL 63

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
            + KQIK+      +PVI +TA +         + G   Y+ KP  +   +  +++ I
Sbjct: 64  ALLKQIKQ--RHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAI 119


>3n0r_A Response regulator; sigma factor, receiver, two-component SI
           transduction, signaling protein; HET: MSE GOL; 1.25A
           {Caulobacter vibrioides}
          Length = 286

 Score = 85.0 bits (210), Expect = 4e-18
 Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 11/122 (9%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKPDVIIMDIQ-LQE 58
           +  +V+I+ED  +       L+   G+          EALE   +  P +++ DIQ    
Sbjct: 159 LATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADG 218

Query: 59  ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIR--KGGCEAYISKPISLSIFMETI 116
            SG++  K I       ++PVI +TAF     E  +   +      I+KP         I
Sbjct: 219 SSGIDAVKDILGRM---DVPVIFITAF----PERLLTGERPEPTFLITKPFQPETVKAAI 271

Query: 117 KK 118
            +
Sbjct: 272 GQ 273


>3cu5_A Two component transcriptional regulator, ARAC family; structural
           genomics, protein structure initiative; 2.60A
           {Clostridium phytofermentans isdg}
          Length = 141

 Score = 85.0 bits (210), Expect = 4e-18
 Identities = 29/123 (23%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGY---IALQTRNGMEALELARQHKPDVIIMDIQLQ 57
           M  +++IV+D +L        I           Q  +G+ A+++A +H P+V++ D+++ 
Sbjct: 1   MSLRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIALKHPPNVLLTDVRMP 60

Query: 58  EISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
            + G+E+   I +     +  VI ++ ++ K   +   K     Y+ KPI  S  M+ +K
Sbjct: 61  RMDGIELVDNILK--LYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALK 118

Query: 118 KYI 120
           + I
Sbjct: 119 QSI 121


>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock,
           transferase, response regulator, histidine protein
           kinase; NMR {Synechococcus elongatus}
          Length = 119

 Score = 84.7 bits (209), Expect = 4e-18
 Identities = 18/117 (15%), Positives = 51/117 (43%), Gaps = 3/117 (2%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            ++++E+ +    +  +++  +G+  +   +G  AL+     +P VI+M     + S L 
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDLLQPIVILMAWPPPDQSCLL 62

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + + ++E       P++       +   + +      A +SKP+   + + T++   
Sbjct: 63  LLQHLREHQADPHPPLVLFLG---EPPVDPLLTAQASAILSKPLDPQLLLTTLQGLC 116


>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II,
           respose regulator, protein structure initiative; 2.40A
           {Rhodospirillum rubrum atcc 11170}
          Length = 152

 Score = 84.4 bits (208), Expect = 6e-18
 Identities = 26/129 (20%), Positives = 60/129 (46%), Gaps = 11/129 (8%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYI-----------ALQTRNGMEALELARQHKPDV 49
           +   ++++ED+  + +L    I  +G             AL    G +        +  +
Sbjct: 3   LSVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQL 62

Query: 50  IIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISL 109
           +++D+ L +++G++I K +KE+   +  PV+ +T    + + +R    G   YI+KP++ 
Sbjct: 63  VLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNY 122

Query: 110 SIFMETIKK 118
             F   I++
Sbjct: 123 ENFANAIRQ 131


>3hdv_A Response regulator; PSI-II, structural genomics, protein structure
           initiative, NEW YORK SGX research center for structural
           genomics; 2.09A {Pseudomonas putida KT2440}
          Length = 136

 Score = 84.2 bits (208), Expect = 7e-18
 Identities = 27/119 (22%), Positives = 57/119 (47%), Gaps = 2/119 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQEISG 61
             V++V+DN +N +     +++ G  A+      EA   L  Q +  ++I D+++Q  SG
Sbjct: 8   PLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQKRIGLMITDLRMQPESG 67

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           L++ + I+   E   + +I V+      +   +   G   ++ KP+ L   +E + K +
Sbjct: 68  LDLIRTIRAS-ERAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKEL 125


>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+
           ATPase, response regulator, transcriptional activator,
           ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB:
           1zit_A 2jrl_A
          Length = 368

 Score = 84.1 bits (208), Expect = 7e-18
 Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 2/118 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           K+V++V+D E        ++E  GY     +   EA +  ++    VI++D+ + +  G+
Sbjct: 1   KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGV 60

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
                IKE+S   +  VI +T         +  K G   ++ KP S+  F+ TIK   
Sbjct: 61  NFIDFIKENS--PDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAF 116


>2qsj_A DNA-binding response regulator, LUXR family; structural genomics,
           PSI-2, protein structure initiative; 2.10A {Silicibacter
           pomeroyi dss-3}
          Length = 154

 Score = 83.9 bits (207), Expect = 9e-18
 Identities = 22/120 (18%), Positives = 47/120 (39%), Gaps = 5/120 (4%)

Query: 2   LKKVMIVEDNELNMKLFRDLIET--SGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQE 58
           L  V+IV+D+ L     ++L+E   SG          +AL  L   +  D+I++D+ L +
Sbjct: 3   LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNLPD 62

Query: 59  ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
              ++   ++K         V  ++            + G + +I K     + +  +  
Sbjct: 63  AEAIDGLVRLKRFD--PSNAVALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSL 120


>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC,
           target 11006U, PSI-2, protein structure initiative;
           2.00A {Desulfuromonas acetoxidans dsm 684}
          Length = 147

 Score = 82.8 bits (204), Expect = 2e-17
 Identities = 28/117 (23%), Positives = 62/117 (52%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           ++M+V+     +      +   G+  +Q  N +EA+ +A +  P +II +  + +ISG++
Sbjct: 10  RIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMD 69

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           +   +K++ +   IPVIA++  A   +E ++   G   +I+KP++       IK+ +
Sbjct: 70  LFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVL 126


>3cz5_A Two-component response regulator, LUXR family; structural genomics,
           protein structure initiative; 2.70A {Aurantimonas SP}
          Length = 153

 Score = 82.4 bits (203), Expect = 2e-17
 Identities = 26/117 (22%), Positives = 56/117 (47%), Gaps = 4/117 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           ++M+V+D+ +  + +R LIE     A+  +  +  EA  L R+  PD+++MD+ L    G
Sbjct: 7   RIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGG 66

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           +E T+ I++        ++  T         +  + G   Y++K    +  ++ I+ 
Sbjct: 67  IEATRHIRQWD--GAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEA 121


>3cg4_A Response regulator receiver domain protein (CHEY- like); structural
           genomics, unknown function, uncharacterized protein;
           HET: MSE; 1.61A {Methanospirillum hungatei jf-1}
          Length = 142

 Score = 82.1 bits (202), Expect = 3e-17
 Identities = 24/119 (20%), Positives = 56/119 (47%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             VMIV+D+       + ++  +G+  +   +G + ++L ++    V+++DI +  + G 
Sbjct: 8   GDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGW 67

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIG 121
           +  + I ++S  Q I ++ +TA      +    +     YI+KP      +E    ++G
Sbjct: 68  DTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMG 126


>2gkg_A Response regulator homolog; social motility, receiver domain,
           signalling, high resolution, signaling protein; 1.00A
           {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A
          Length = 127

 Score = 82.0 bits (202), Expect = 3e-17
 Identities = 29/122 (23%), Positives = 60/122 (49%), Gaps = 2/122 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIM-DIQLQEI 59
           M KK++IVE +       R  +E  G+   +T +G  ++E  R+ +PD++++        
Sbjct: 4   MSKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQ 63

Query: 60  SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
           +G  I  ++K+D +L+ +P++ +        + R  K   + Y++KP+     +E     
Sbjct: 64  NGYLICGKLKKDDDLKNVPIVIIGNPDGF-AQHRKLKAHADEYVAKPVDADQLVERAGAL 122

Query: 120 IG 121
           IG
Sbjct: 123 IG 124


>3luf_A Two-component system response regulator/ggdef domain protein;
           structural genomics, ASA_2441, PSI-2, protein structure
           initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB:
           3mf4_A*
          Length = 259

 Score = 82.0 bits (202), Expect = 3e-17
 Identities = 20/118 (16%), Positives = 51/118 (43%), Gaps = 1/118 (0%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKP-DVIIMDIQLQEISGL 62
           +V++V+D+  +       +        +  +  EAL    QH    ++++D  + EI G+
Sbjct: 126 EVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGI 185

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
            + + ++E    Q++ +I ++    +G   R  K G   ++++P         +   +
Sbjct: 186 SLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNL 243



 Score = 60.5 bits (146), Expect = 1e-10
 Identities = 12/68 (17%), Positives = 30/68 (44%)

Query: 1  MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
          + +K++IVED+    ++    I     + +   + +E     +  +  V ++D+ L +  
Sbjct: 3  LKQKILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHCQGDEYVVALVDLTLPDAP 62

Query: 61 GLEITKQI 68
            E  K +
Sbjct: 63 SGEAVKVL 70


>3kto_A Response regulator receiver protein; PSI-II,structural genomics,
           protein structure initiative; 1.98A {Pseudoalteromonas
           atlantica T6C}
          Length = 136

 Score = 82.0 bits (202), Expect = 3e-17
 Identities = 13/120 (10%), Positives = 36/120 (30%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            + +V+  +        L+           +    +          +I++  L++     
Sbjct: 8   IIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSG 67

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIGEA 123
           I            +P I + + +      R  +     +I KP    + +  +++ I  A
Sbjct: 68  IELLETLVKRGFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGA 127


>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex,
           response regulator, receiver domain, two-component
           signal transduction; HET: BFD; 1.96A {Borrelia
           burgdorferi}
          Length = 157

 Score = 81.6 bits (201), Expect = 4e-17
 Identities = 24/121 (19%), Positives = 55/121 (45%), Gaps = 5/121 (4%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKP--DVIIMDIQLQ 57
           +   V+IV+D+   +K    +  + G+  + T  +G EA+   + H P  D++ + I + 
Sbjct: 35  IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMP 94

Query: 58  EISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
           ++ G+     I E    +   VI ++A   +   +     G + +I KP+  +  ++ + 
Sbjct: 95  KMDGITCLSNIMEFD--KNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVM 152

Query: 118 K 118
            
Sbjct: 153 S 153


>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein
           structure initiative; 2.40A {Klebsiella pneumoniae}
          Length = 143

 Score = 81.5 bits (201), Expect = 5e-17
 Identities = 28/119 (23%), Positives = 54/119 (45%), Gaps = 6/119 (5%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           KV+IVED  L  +    LI T   + +     +G++ L+  + +K D I +DI +  + G
Sbjct: 11  KVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQHNKVDAIFLDINIPSLDG 70

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + + + I + +   +  ++ +T  A K       +     YI KP   S  +  ++K  
Sbjct: 71  VLLAQNISQFA--HKPFIVFIT--AWKEHAVEAFELEAFDYILKPYQESRIINMLQKLT 125


>2b4a_A BH3024; 10175646, structural genomics, joint center for structural
           genomics, JCSG, protein structure initiative PSI,
           unknown function; 2.42A {Bacillus halodurans c-125}
           SCOP: c.23.1.1
          Length = 138

 Score = 81.1 bits (200), Expect = 6e-17
 Identities = 21/117 (17%), Positives = 48/117 (41%), Gaps = 6/117 (5%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALE-LARQHKPDVIIMDIQLQEISGL 62
           +V +VED   +  L +  +   G       +G    +  ++    D++I+  QL ++S  
Sbjct: 17  RVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIF 76

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
            +   +KE +  ++  V+ +T      +     +     Y+ KP ++S     I  +
Sbjct: 77  SLLDIVKEQT--KQPSVLILTTGRH--ELIESSEHNLS-YLQKPFAISELRAAIDYH 128


>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine
           hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1
           c.40.1.1
          Length = 349

 Score = 81.3 bits (200), Expect = 6e-17
 Identities = 19/107 (17%), Positives = 53/107 (49%), Gaps = 3/107 (2%)

Query: 4   KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           +V+ V+D+ L  ++  ++I +     +     + + A +L ++  PDV+ +D+++  + G
Sbjct: 5   RVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDG 64

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPIS 108
           L+  +++     +  + V ++T    +    R  + G   +++KP  
Sbjct: 65  LDFLEKLMRLRPMPVVMVSSLTGKGSE-VTLRALELGAIDFVTKPQL 110


>3eqz_A Response regulator; structural genomics, unknown function, PSI-2,
           protein structure initiative; 2.15A {Colwellia
           psychrerythraea 34H}
          Length = 135

 Score = 80.8 bits (199), Expect = 8e-17
 Identities = 21/123 (17%), Positives = 48/123 (39%), Gaps = 8/123 (6%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            +V IV+D+ L   L + ++E       +      A      +K D+II+D+ + ++ G+
Sbjct: 4   NRVFIVDDDTLTCNLLKTIVEPIFGNV-EAFQHPRAFLTLSLNKQDIIILDLMMPDMDGI 62

Query: 63  EITKQIKEDSELQEIPVIAVTAF---AMKGDEERIR--KGGCEAYISKPISLSIFMETIK 117
           E+ + + E        +I ++ +    +   E              +KPI+  +    + 
Sbjct: 63  EVIRHLAEHK--SPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLT 120

Query: 118 KYI 120
              
Sbjct: 121 SLS 123


>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural
           genomics, protein structure initiative; 1.50A
           {Legionella pneumophila subsp}
          Length = 143

 Score = 80.4 bits (198), Expect = 9e-17
 Identities = 22/122 (18%), Positives = 57/122 (46%), Gaps = 8/122 (6%)

Query: 4   KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALEL------ARQHKPDVIIMDIQ 55
            ++ +ED+E++++    +             ++G +AL++        +  P +I++DI 
Sbjct: 9   DILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLDIN 68

Query: 56  LQEISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMET 115
           + +++G+E  K++++DS   +I V  +TA     D+          ++ KP+     ++ 
Sbjct: 69  IPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKL 128

Query: 116 IK 117
             
Sbjct: 129 FW 130


>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE
           PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*
          Length = 116

 Score = 80.0 bits (197), Expect = 1e-16
 Identities = 29/118 (24%), Positives = 61/118 (51%), Gaps = 4/118 (3%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           K++++V+D     +L ++ ++  GY      NG EAL+       D++I+DI++  ISGL
Sbjct: 2   KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFFSGNYDLVILDIEMPGISGL 61

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           E+  +I++    ++  +I +TA++       +     + Y+ K  +     E +KK +
Sbjct: 62  EVAGEIRKKK--KDAKIILLTAYSH--YRSDMSSWAADEYVVKSFNFDELKEKVKKLL 115


>3c3m_A Response regulator receiver protein; structural genomics, unknown
           function, PSI-2, protein structure initiative; HET: MSE;
           1.70A {Methanoculleus marisnigri JR1}
          Length = 138

 Score = 80.2 bits (197), Expect = 1e-16
 Identities = 32/118 (27%), Positives = 62/118 (52%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             +++V+D+ + + +F  ++E  GY  +   +G E LE      PD++++DI ++ + G 
Sbjct: 4   YTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGW 63

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           E  ++IK D   ++IPV+ +TA  +  +E        E YI KP +     E I+  +
Sbjct: 64  ETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVL 121


>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54
           activator, bacterial transcription, dimer; HET: ADP;
           2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB:
           1ny6_A* 1zy2_A*
          Length = 387

 Score = 79.9 bits (197), Expect = 1e-16
 Identities = 33/116 (28%), Positives = 55/116 (47%), Gaps = 2/116 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            V+++ED+++   L  + +   G        G EA +L  +   +V+++D+ L +++GLE
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLE 61

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
           I K IKE S   E  VI +T            K G   +++KP  L     TI K 
Sbjct: 62  ILKWIKERS--PETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKA 115


>2a9o_A Response regulator; essential protein, YYCF/YYCG homolog, signaling
           protein; 1.65A {Streptococcus pneumoniae} SCOP: c.23.1.1
           PDB: 1nxo_A 1nxs_A 1nxv_A 1nxw_A 1nxx_A 1nxp_A 2a9p_A
           2a9q_A 1nxt_A* 2a9r_A*
          Length = 120

 Score = 78.8 bits (194), Expect = 3e-16
 Identities = 36/118 (30%), Positives = 64/118 (54%), Gaps = 3/118 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           KK++IV+D +    + +  +   GY  +   NG EALE     +PD+II+D+ L EI GL
Sbjct: 2   KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGL 61

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           E+ K I++ S    +P++ ++A   + D+    + G + Y++KP S       +K  +
Sbjct: 62  EVAKTIRKTS---SVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALL 116


>3eod_A Protein HNR; response regulator, phosphoprotein, two-component
           regulatory system, signaling protein; 1.75A {Escherichia
           coli K12}
          Length = 130

 Score = 78.5 bits (193), Expect = 4e-16
 Identities = 30/119 (25%), Positives = 60/119 (50%), Gaps = 3/119 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
           K+++IVED ++   L      + G   +   +G++ALEL     PD++I DI +  ++GL
Sbjct: 8   KQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICDIAMPRMNGL 67

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPIS-LSIFMETIKKYI 120
           ++ + I+      + PV+ ++A     D  +  + G E  + KP+  L+   E +   +
Sbjct: 68  KLLEHIRNRG--DQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACL 124


>3cg0_A Response regulator receiver modulated diguanylate cyclase with
           PAS/PAC sensor; signal receiver domain; 2.15A
           {Desulfovibrio desulfuricans subsp}
          Length = 140

 Score = 77.8 bits (191), Expect = 6e-16
 Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 5/121 (4%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQHKPDVIIMDI-QLQEI 59
           L  V+IVED  L     R  +E+ GY  L    NG EA+  A   +PD+ ++DI     +
Sbjct: 9   LPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGAL 68

Query: 60  SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKY 119
            G+E   ++        +P+I +T+       +R ++     Y++KP++      +I+  
Sbjct: 69  DGVETAARLAAGCN---LPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMA 125

Query: 120 I 120
           I
Sbjct: 126 I 126


>3cfy_A Putative LUXO repressor protein; structural genomics, unknown
           function, uncharacterized protein, signal receiver
           domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}
          Length = 137

 Score = 77.1 bits (189), Expect = 1e-15
 Identities = 26/120 (21%), Positives = 58/120 (48%), Gaps = 2/120 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           +  +V++VED+     L++  ++   Y       G +A++   + KP +II+D++L ++S
Sbjct: 3   LRPRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMS 62

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G ++   I ++       VI  TA         + + G E ++ KPI+      ++  ++
Sbjct: 63  GEDVLDWINQND--IPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHL 120


>3gt7_A Sensor protein; structural genomics, signal receiver domain,
           kinase, PSI-2, protein structure initiative; 2.30A
           {Syntrophus aciditrophicus SB}
          Length = 154

 Score = 74.1 bits (181), Expect = 9e-15
 Identities = 33/117 (28%), Positives = 63/117 (53%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           +++IVED+    +  + ++E +GY     RNG EA+      +PD+II D+ + E+ G  
Sbjct: 9   EILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYA 68

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + + +K   +L+ IPVI +T  +   D  R  + G + +I+KP    +    +K+ +
Sbjct: 69  LCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLL 125


>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response
           regulator, four helix bundle, histidine phosphotransfer
           (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP:
           c.23.1.1 PDB: 1oxk_B 1oxb_B
          Length = 133

 Score = 73.5 bits (180), Expect = 1e-14
 Identities = 31/123 (25%), Positives = 64/123 (52%), Gaps = 7/123 (5%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQT-RNGMEALELARQ-----HKPDVIIMDIQLQ 57
           K+++VEDN +N ++ + ++   G   ++   +G EA +  ++        ++I MD+Q+ 
Sbjct: 4   KILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMP 63

Query: 58  EISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
           ++ GL  TK I+ D      P++A+TAFA   + +   + G   ++SKPI        + 
Sbjct: 64  KVDGLLSTKMIRRDLGYT-SPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILT 122

Query: 118 KYI 120
           ++ 
Sbjct: 123 EFC 125


>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein
           structure initiative II (PSI II), structural genomics;
           1.95A {Thermotoga maritima}
          Length = 142

 Score = 73.6 bits (180), Expect = 1e-14
 Identities = 30/120 (25%), Positives = 57/120 (47%), Gaps = 3/120 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           +   VM+V+++ +     ++ +E  G+  +  +N  EA    R+ K D++ +D   +   
Sbjct: 3   LTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLRREKIDLVFVD-VFEGEE 61

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
            L + ++I+E  E  +  V  ++A+  K       K G   YI KP  L   +E +KK I
Sbjct: 62  SLNLIRRIRE--EFPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKII 119


>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component
           system, gene regulation, transcription factor, KDP
           potassium transport system; 2.00A {Escherichia coli}
           SCOP: c.23.1.1 PDB: 1zh4_A
          Length = 121

 Score = 72.8 bits (178), Expect = 2e-14
 Identities = 29/116 (25%), Positives = 54/116 (46%), Gaps = 3/116 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             V+IVED +   +  R  +E  G    +       L  A   KPD+II+D+ L +  G+
Sbjct: 2   TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGI 61

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           E  + +++      +PVI ++A + + D+      G + Y+SKP  +      ++ 
Sbjct: 62  EFIRDLRQW---SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRV 114


>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HUPR1;
           nucleotide-binding, transcription regulation; 2.10A
           {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B
          Length = 139

 Score = 72.3 bits (177), Expect = 2e-14
 Identities = 18/116 (15%), Positives = 47/116 (40%), Gaps = 4/116 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            +++V+D   ++   +  +E   +  L  +    A+ +  +    VII D ++   +G++
Sbjct: 3   AILLVDDEPHSLAAMKLALE-DDFDVLTAQGAEAAIAILEEEWVQVIICDQRMPGRTGVD 61

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGD-EERIRKGGCEAYISKPISLSIFMETIKK 118
              +++E     E   I +T +         I   G   +++KP      + + + 
Sbjct: 62  FLTEVRE--RWPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARN 115


>2qr3_A Two-component system response regulator; structural genomics,
           signal receiver, PSI-2, protein structure initiative;
           1.80A {Bacteroides fragilis YCH46}
          Length = 140

 Score = 72.4 bits (177), Expect = 3e-14
 Identities = 27/127 (21%), Positives = 57/127 (44%), Gaps = 7/127 (5%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQE--- 58
           L  ++IV+DN+  +   + L++      +   + +    + R+  P+V+++D+       
Sbjct: 3   LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGIN 62

Query: 59  --ISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETI 116
               GL    +IK   + +++PV+  TA+A      R  K G   ++ KP      +ET+
Sbjct: 63  NGNEGLFWLHEIKR--QYRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETL 120

Query: 117 KKYIGEA 123
                +A
Sbjct: 121 LNAASQA 127


>3h5i_A Response regulator/sensory box protein/ggdef domain protein;
           structural genomics, transcription, PSI-2; 1.90A
           {Carboxydothermus hydrogenoformans z-2901}
          Length = 140

 Score = 71.6 bits (175), Expect = 4e-14
 Identities = 32/120 (26%), Positives = 60/120 (50%), Gaps = 5/120 (4%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELA-RQHKPDVIIMDIQL-QEIS 60
           KK++IVED++   K   +++   GY       G  A+E       PD+I+MDI+L + + 
Sbjct: 6   KKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMD 65

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G++    I++ SE   +PV+ +TA       E+IR      Y+ K  +  + +  ++  +
Sbjct: 66  GVQTALAIQQISE---LPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMAL 122


>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD
           subdomain; structural genomics, oceanospirillum SP.
           MED92, PSI-2; 2.10A {Neptuniibacter caesariensis}
          Length = 154

 Score = 70.8 bits (173), Expect = 7e-14
 Identities = 21/119 (17%), Positives = 54/119 (45%), Gaps = 3/119 (2%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             VM+V+D +  +   + LI+  G   +   + ++ALE  +     ++I D+++ E+ G 
Sbjct: 8   YTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISDMRMPEMGGE 67

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEER-IRKGGCEAYISKPISLSIFMETIKKYI 120
              +Q+ +     +I  + ++ +A        + +G    ++ KP       + ++K +
Sbjct: 68  VFLEQVAK--SYPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGL 124


>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein
           structure initiative, structural genomics; 2.59A
           {Cytophaga hutchinsonii atcc 33406}
          Length = 146

 Score = 70.6 bits (172), Expect = 1e-13
 Identities = 22/132 (16%), Positives = 54/132 (40%), Gaps = 10/132 (7%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIA--LQTRNGMEALELARQ-----HKPDVIIMDI 54
           +  V++++D+++   L   +I  +  +       +G  A+    +       P +I +DI
Sbjct: 9   IDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICIDI 68

Query: 55  QLQEISGLEITKQIKE--DSELQEIPVIAVTAFAMKGDEER-IRKGGCEAYISKPISLSI 111
            +  I+G E+    K+       +  V  +++     D+ +       + Y+SKP++ + 
Sbjct: 69  NMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANA 128

Query: 112 FMETIKKYIGEA 123
                 K + E 
Sbjct: 129 LNNLYNKVLNEG 140


>3crn_A Response regulator receiver domain protein, CHEY- like; structural
           genomics, signal regulator receiver domain; HET: PHD;
           1.58A {Methanospirillum hungatei jf-1}
          Length = 132

 Score = 69.8 bits (170), Expect = 1e-13
 Identities = 28/121 (23%), Positives = 56/121 (46%), Gaps = 2/121 (1%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           LK+++IV+D+   +   + ++E  GY         E L        ++ +  I+L ++ G
Sbjct: 3   LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEFFNLALFXIKLPDMEG 62

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYIG 121
            E+ ++  +      +  I VT +A   +       G +AYI KP++    +E IK+ + 
Sbjct: 63  TELLEKAHKLR--PGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLD 120

Query: 122 E 122
           E
Sbjct: 121 E 121


>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein
           structure initiative; 2.45A {Rhodopirellula baltica}
          Length = 151

 Score = 69.7 bits (170), Expect = 2e-13
 Identities = 20/122 (16%), Positives = 53/122 (43%), Gaps = 5/122 (4%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKP-DVIIMDIQLQEI 59
           + +++++V+D+   +   +  +    +      +G EAL   ++  P  VI++D+++  +
Sbjct: 3   LNERILLVDDDYSLLNTLKRNLS-FDFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGM 61

Query: 60  SGLEITKQIKEDSELQEIPVIAVTAFAMKGDEER-IRKGGCEAYISKPISLSIFMETIKK 118
            G E+ ++ +  S       + +T           + +G    +++KP  +S     I  
Sbjct: 62  EGTEVIQKARLIS--PNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINA 119

Query: 119 YI 120
            I
Sbjct: 120 GI 121


>1zgz_A Torcad operon transcriptional regulatory protein TORR;
           two-component system, gene regulation, transcription
           factor, TMAO respiratory system; 1.80A {Escherichia
           coli} SCOP: c.23.1.1
          Length = 122

 Score = 68.2 bits (166), Expect = 4e-13
 Identities = 29/120 (24%), Positives = 57/120 (47%), Gaps = 3/120 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M   ++IVED  +     +      GY    T +G    E+ +    D+I++DI L + +
Sbjct: 1   MPHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDEN 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           GL +T+ ++E      + +I VT  + + D     + G + Y++KP+ L   +  +K  +
Sbjct: 61  GLMLTRALRER---STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLL 117


>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF,
           half barrel, de novo protein; 3.10A {Thermotoga
           maritima}
          Length = 237

 Score = 67.7 bits (165), Expect = 7e-13
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 26  GYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVIAVTAF 85
             I     NG EA+E  ++ KPD++ MDI + E++G++  K+I +        +I  +A 
Sbjct: 5   VLIVDDATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKID--PNAKIIVCSAM 62

Query: 86  AMKGDEERIRKGGCEAYISKPISL 109
             +       K G + +I    ++
Sbjct: 63  GQQAMVIEAIKAGAKDFIVNTAAV 86


>1xhf_A DYE resistance, aerobic respiration control protein ARCA;
           two-component system, gene regulation, transcription
           factor, anoxic redox control; 2.15A {Escherichia coli}
           SCOP: c.23.1.1 PDB: 1xhe_A
          Length = 123

 Score = 67.5 bits (164), Expect = 7e-13
 Identities = 24/117 (20%), Positives = 52/117 (44%), Gaps = 3/117 (2%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            ++IVED  +     + + E  GY   +  +G E  ++  ++  +++IMDI L   +G  
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNG-- 62

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
                +E  E   + ++ +T    + D+    + G + YI+KP +        +  +
Sbjct: 63  -LLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLL 118


>2qzj_A Two-component response regulator; 11017X, PSI-II, structural
           genomics, protein structure initiative; 2.89A
           {Clostridium difficile 630}
          Length = 136

 Score = 67.5 bits (164), Expect = 8e-13
 Identities = 25/120 (20%), Positives = 54/120 (45%), Gaps = 3/120 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           +  K++I++ ++ N +  +  +E  G       N  EA+     +K D+I ++I L +  
Sbjct: 3   LQTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGD 62

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G  + K+I+  +     P++ +T              G + Y+ KP++L I    +K  +
Sbjct: 63  GWTLCKKIRNVT---TCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAIL 119


>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded
           beta/alpha fold, nitrogen fixation regulation; HET: 15P;
           1.60A {Rhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A*
           1dcm_A 1d5w_A*
          Length = 126

 Score = 67.4 bits (164), Expect = 9e-13
 Identities = 25/116 (21%), Positives = 52/116 (44%), Gaps = 2/116 (1%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
             V IV+D E   K    ++  +G+     ++    L  A   +  V++ D+++ ++SG+
Sbjct: 4   YTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGV 63

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           E+ + + +      IP I +T            K G   +I KP   ++ +E I++
Sbjct: 64  ELLRNLGDLK--INIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIER 117


>2rdm_A Response regulator receiver protein; structural genomics, unknown
           function, PSI-2, protein structure initiative; HET: MSE;
           1.76A {Sinorhizobium medicae WSM419}
          Length = 132

 Score = 67.0 bits (163), Expect = 1e-12
 Identities = 17/119 (14%), Positives = 51/119 (42%), Gaps = 6/119 (5%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKP-DVIIMDIQ-LQEISG 61
            +++ +D  + +  F   +  +G++     +G +A+E+ +     D ++ DI+  Q   G
Sbjct: 7   TILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDG 66

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
            ++ +  +E      +P++ ++  A    E           + KP + +  +  + + +
Sbjct: 67  WQVARVARE--IDPNMPIVYISGHAA--LEWASNGVPDSIILEKPFTSAQLITAVSQLL 121


>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response
           regulator, beryllium fluoride, transcription factor,
           activated, virulence; 1.90A {Escherichia coli} SCOP:
           c.23.1.1 PDB: 2pkx_A
          Length = 121

 Score = 66.7 bits (162), Expect = 1e-12
 Identities = 27/115 (23%), Positives = 55/115 (47%), Gaps = 2/115 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           +V++VEDN L     +  I+ +G+      +  EA     +H PD+ I+D+ L +  GL 
Sbjct: 2   RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLS 61

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
           + ++ + +     I  + +TA     D+  +   G + Y++KP  +   M  ++ 
Sbjct: 62  LIRRWRSNDVSLPI--LVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQA 114


>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas
           aeruginosa} SCOP: c.23.1.3
          Length = 196

 Score = 62.9 bits (152), Expect = 2e-11
 Identities = 13/117 (11%), Positives = 31/117 (26%), Gaps = 7/117 (5%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           +V+++             +   G    Q     EA +       DV+   I         
Sbjct: 14  QVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD----VPVDVVFTSIFQNRHHDEI 69

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
                          ++A+  +       +I +  C   I++P+     +  +    
Sbjct: 70  AALLAAGTP---RTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSAR 123


>3klo_A Transcriptional regulator VPST; REC domain, HTH domain,
           DNA-binding, transcription regulation; HET: C2E TAR;
           2.80A {Vibrio cholerae} PDB: 3kln_A*
          Length = 225

 Score = 62.4 bits (151), Expect = 2e-11
 Identities = 10/118 (8%), Positives = 33/118 (27%), Gaps = 4/118 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTR---NGMEALELARQHKPDVIIMDIQLQEIS 60
            V ++ D  +  +L ++ +E+   +AL+                    ++++D       
Sbjct: 9   NVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRSIQMLVIDYSRISDD 68

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKK 118
            L      K      +   + +        +   +             +   ++ + K
Sbjct: 69  VLTDYSSFKHI-SCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSK 125


>2gwr_A DNA-binding response regulator MTRA; two-component regulatory
           system, transcription regulation, phosphorylation, OMPR
           family; 2.10A {Mycobacterium tuberculosis}
          Length = 238

 Score = 61.7 bits (149), Expect = 4e-11
 Identities = 23/123 (18%), Positives = 61/123 (49%), Gaps = 9/123 (7%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M +++++V+D+    ++   ++   G+      +G +AL   R+ +PD++++D+ L  ++
Sbjct: 4   MRQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVRELRPDLVLLDLMLPGMN 63

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPISLSIFMETIK 117
           G+++ + ++ DS +  + +        K D   +  G   G + YI KP      +  ++
Sbjct: 64  GIDVCRVLRADSGVPIVMLT------AKTDTVDVVLGLESGADDYIMKPFKPKELVARVR 117

Query: 118 KYI 120
             +
Sbjct: 118 ARL 120


>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein,
           ALPH-beta sandwich, winged-helix, helix-turn-helix, DNA
           binding protein; HET: DNA MSE; 1.50A {Thermotoga
           maritima} SCOP: a.4.6.1 c.23.1.1
          Length = 225

 Score = 59.1 bits (142), Expect = 3e-10
 Identities = 30/120 (25%), Positives = 53/120 (44%), Gaps = 2/120 (1%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M  +V++VED      L  + ++   +      +G E + +A     DV+I+DI L    
Sbjct: 1   MNVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHD 60

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G EI K ++E       PV+ +TA +      +    G + Y+ KP  L   +  ++  I
Sbjct: 61  GWEILKSMRESG--VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALI 118


>2oqr_A Sensory transduction protein REGX3; response regulator,
           winged-helix-turn-helix, DNA-binding, 3D domain
           swapping; 2.03A {Mycobacterium tuberculosis H37RV}
          Length = 230

 Score = 58.9 bits (142), Expect = 3e-10
 Identities = 32/113 (28%), Positives = 55/113 (48%), Gaps = 3/113 (2%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M   V+IVED E        L+   G+ A    +G  AL    +   D++++D+ L  +S
Sbjct: 3   MATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMS 62

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFM 113
           G ++ KQ++       +PVI VTA   + D+    + G + Y++KP S    +
Sbjct: 63  GTDVCKQLRAR---SSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARELI 112


>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A
           {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1
          Length = 220

 Score = 58.2 bits (140), Expect = 4e-10
 Identities = 28/120 (23%), Positives = 60/120 (50%), Gaps = 5/120 (4%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEIS 60
           M+ K+ +V+D++  +K   + ++  G +      G + L    +    V+++D+ L + S
Sbjct: 1   MMWKIAVVDDDKNILKKVSEKLQQLGRVK-TFLTGEDFLN--DEEAFHVVVLDVMLPDYS 57

Query: 61  GLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           G EI + IKE     E  VI +T  +      +  + G + Y++KP +  I +  +K+++
Sbjct: 58  GYEICRMIKETR--PETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFL 115


>1yio_A Response regulatory protein; transcription regulation, DNA binding
           protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2
           c.23.1.1 PDB: 1zn2_A
          Length = 208

 Score = 57.3 bits (137), Expect = 9e-10
 Identities = 25/117 (21%), Positives = 56/117 (47%), Gaps = 2/117 (1%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
            V +V+D+    +  R+L+ ++G+           LE  R  +   +++D+++  +SG+E
Sbjct: 6   TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIE 65

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           + +Q+   S    IP++ +TA        R  K G   ++ KP      ++ I++ +
Sbjct: 66  LQEQLTAIS--DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGL 120


>3jte_A Response regulator receiver protein; structural genomics, nysgrc,
           response regulator receiver domain, target 11226E,
           PSI-2; 1.90A {Clostridium thermocellum atcc 27405}
          Length = 143

 Score = 57.1 bits (137), Expect = 1e-09
 Identities = 19/119 (15%), Positives = 45/119 (37%)

Query: 2   LKKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
           L K+++++D    ++  + L+E  G   L   +  E L +  ++   + ++   ++    
Sbjct: 3   LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKL 62

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
             +    +       + VI +T      +     K G   Y+ KP++       I   I
Sbjct: 63  SGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAI 121


>3c3w_A Two component transcriptional regulatory protein DEVR; response
          regulator, two-component regulatory system, DNA-
          binding protein; 2.20A {Mycobacterium tuberculosis}
          Length = 225

 Score = 51.5 bits (122), Expect = 6e-08
 Identities = 15/60 (25%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 4  KVMIVEDNELNMKLFRDLIETSGYIAL--QTRNGMEALELARQHKPDVIIMDIQLQEISG 61
          KV +V+D+E+  +   DL+     + +  +  +  EA+      +PDV ++D++L + +G
Sbjct: 3  KVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNG 62


>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter
           pylori} PDB: 2hqo_A
          Length = 137

 Score = 51.3 bits (122), Expect = 6e-08
 Identities = 18/115 (15%), Positives = 45/115 (39%), Gaps = 7/115 (6%)

Query: 4   KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLE 63
           +V+++E N +        +   G++A  T +  +   L      D++++           
Sbjct: 20  RVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVMVSD------KNA 73

Query: 64  ITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPI-SLSIFMETIK 117
           ++   +   +   I V+  +      +E    + G + YI+KP  S+   +  I+
Sbjct: 74  LSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIE 128


>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA
           binding domain, phosphorylation; 1.58A {Mycobacterium
           tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A
          Length = 233

 Score = 50.3 bits (119), Expect = 1e-07
 Identities = 24/120 (20%), Positives = 53/120 (44%), Gaps = 8/120 (6%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGL 62
            +V++V+D+   +      +  SG+      +G EAL  A +++PD I++DI +  + G+
Sbjct: 8   PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENRPDAIVLDINMPVLDGV 67

Query: 63  EITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKG---GCEAYISKPISLSIFMETIKKY 119
            +   ++          + V   + +   +    G   G + Y+ KP  L+  +  +K  
Sbjct: 68  SVVTALR-----AMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKAL 122


>2hqr_A Putative transcriptional regulator; phosporylation-independent
          response regulator, H. pylori, symmetric dimer,
          signaling protein; NMR {Helicobacter pylori J99}
          Length = 223

 Score = 44.7 bits (104), Expect = 5e-06
 Identities = 8/52 (15%), Positives = 23/52 (44%)

Query: 4  KVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQ 55
          +V+++E N +        +   G++A  T +  +   L      D++++  +
Sbjct: 2  RVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLVMVSDK 53


>1a04_A Nitrate/nitrite response regulator protein NARL; signal
           transduction protein, response regulators, two-
           component systems; 2.20A {Escherichia coli} SCOP:
           a.4.6.2 c.23.1.1 PDB: 1rnl_A
          Length = 215

 Score = 43.4 bits (101), Expect = 1e-05
 Identities = 18/119 (15%), Positives = 51/119 (42%), Gaps = 4/119 (3%)

Query: 4   KVMIVEDNELNMKLFRDLIETSG--YIALQTRNGMEALELARQHKPDVIIMDIQLQEISG 61
            +++++D+ +     + LI  +    +  +  NG + +ELA    PD+I++D+ +  ++ 
Sbjct: 7   TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMN- 65

Query: 62  LEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
             +    K   +     ++  +    + D     K G + Y+ K +     ++ + +  
Sbjct: 66  -GLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAA 123


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 32.3 bits (72), Expect = 0.033
 Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 12/37 (32%)

Query: 2  LKKVMIVEDNELNMKLFRDLIETSGYIALQ-TRNGME 37
          LKK+      + ++KL+ D  +++  +A++ T   ME
Sbjct: 22 LKKL------QASLKLYAD--DSAPALAIKAT---ME 47



 Score = 29.6 bits (65), Expect = 0.20
 Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 6/33 (18%)

Query: 57 QEISGLEIT-KQIKEDSELQEIPVIAVTAFAMK 88
          Q +  L+ + K   +DS     P +A+ A  M+
Sbjct: 20 QALKKLQASLKLYADDSA----PALAIKA-TME 47


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 30.7 bits (69), Expect = 0.088
 Identities = 20/82 (24%), Positives = 27/82 (32%), Gaps = 29/82 (35%)

Query: 17  LFRDLIETSGYIALQTRNGMEAL-ELARQHKPDVII------MDIQLQEISGLEITKQIK 69
           L  DLI+ S           E L EL R              ++I L+ +     T    
Sbjct: 183 LVGDLIKFSA----------ETLSELIRT--TLDAEKVFTQGLNI-LEWLENPSNTP--- 226

Query: 70  EDSE-LQEIPV----IAVTAFA 86
            D + L  IP+    I V   A
Sbjct: 227 -DKDYLLSIPISCPLIGVIQLA 247


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
            acid synthase, acyl-carrier-protein, beta-ketoacyl
            reductase, beta-ketoacyl synthase, dehydratase; 4.00A
            {Saccharomyces cerevisiae}
          Length = 1688

 Score = 29.8 bits (66), Expect = 0.18
 Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 13   LNMKLF-RDLIETSGYIALQTRNGMEALELARQHKPDVIIMDIQLQEISGLEITKQIKED 71
            LNMK   R L+     I     N +EAL+L  +  P       + Q    LE T++I  +
Sbjct: 1244 LNMKYRKRQLVTREAQIKDWVENELEALKLEAEEIPS------EDQNEFLLERTREIHNE 1297

Query: 72   SELQ 75
            +E Q
Sbjct: 1298 AESQ 1301


>3mje_A AMPHB; rossmann fold, oxidoreductase; HET: NDP; 1.36A {Streptomyces
           nodosus} PDB: 3mjc_A* 3mjs_A* 3mjv_A* 3mjt_A*
          Length = 496

 Score = 28.8 bits (64), Expect = 0.33
 Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 6/54 (11%)

Query: 5   VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELA-RQHKPDVIIMDIQLQ 57
           V +  D E+      D +   G +A++  + + AL+           I  +  +
Sbjct: 420 VGMATDPEV-----HDRLVRQGVLAMEPEHALGALDQMLENDDTAAAITLMDWE 468


>3g25_A Glycerol kinase; IDP00743, ATP-binding, glycerol metabolism,
           nucleotide-binding, transferase, structural genomics;
           HET: MSE; 1.90A {Staphylococcus aureus subsp} PDB:
           3ge1_A*
          Length = 501

 Score = 27.8 bits (61), Expect = 0.74
 Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 3/37 (8%)

Query: 17  LFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMD 53
             R  +E    +  QTR+ MEA+          + +D
Sbjct: 378 FIRATLE---SLCYQTRDVMEAMSKDSGIDVQSLRVD 411


>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
           topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
           aureus} PDB: 2xcr_B* 2xcq_A* 2xco_A*
          Length = 692

 Score = 26.4 bits (58), Expect = 1.9
 Identities = 10/26 (38%), Positives = 17/26 (65%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I+D++L+ ++GLE  K   E +EL  
Sbjct: 626 ILDMRLRRLTGLERDKIEAEYNELLN 651


>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
           baumannii} PDB: 2xkk_A*
          Length = 767

 Score = 26.1 bits (57), Expect = 2.2
 Identities = 7/26 (26%), Positives = 15/26 (57%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I++++L+ ++ LE  +   E  EL  
Sbjct: 685 ILELKLRHLAKLEEMEIRHEQDELSA 710


>2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA;
           2.80A {Staphylococcus aureus}
          Length = 514

 Score = 26.1 bits (57), Expect = 2.2
 Identities = 7/26 (26%), Positives = 13/26 (50%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I+ +QL  ++  +I     E  EL+ 
Sbjct: 443 IVMLQLYRLTNTDIVALEGEHKELEA 468


>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE
          motif, hydrolase; 1.50A {Bacillus halodurans c-125}
          SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A
          2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A*
          2r7y_A*
          Length = 142

 Score = 26.0 bits (57), Expect = 2.3
 Identities = 6/38 (15%), Positives = 10/38 (26%), Gaps = 6/38 (15%)

Query: 22 IETSGYIALQTRNGME------ALELARQHKPDVIIMD 53
          +     I + T N  E       L   ++      I  
Sbjct: 40 LFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKPIYS 77


>3ilw_A DNA gyrase subunit A; DNA topology, topoisomerase, antibiotic
           resistance, breakage-reunion domain, structural
           genomics; HET: DNA; 1.60A {Mycobacterium tuberculosis}
          Length = 470

 Score = 25.7 bits (56), Expect = 3.2
 Identities = 7/26 (26%), Positives = 18/26 (69%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I+D+QL+ ++ LE  + I + ++++ 
Sbjct: 405 ILDMQLRRLAALERQRIIDDLAKIEA 430


>2otd_A Glycerophosphodiester phosphodiesterase; structural genomics,
          MCSG, PSI-2, protein structure initiative, midwest
          center for structural genomics; 2.60A {Shigella
          flexneri}
          Length = 247

 Score = 25.4 bits (54), Expect = 3.4
 Identities = 7/31 (22%), Positives = 15/31 (48%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G   L   N + A+++  ++   +I  D +L
Sbjct: 14 GGGKLAPENTLAAIDVGAKYGHKMIEFDAKL 44


>3ch0_A Glycerophosphodiester phosphodiesterase; YP_677622.1,
          glycerophosphoryl diester phosphodiesterase, structural
          genomics; HET: MSE CIT GOL; 1.50A {Cytophaga
          hutchinsonii atcc 33406}
          Length = 272

 Score = 25.4 bits (54), Expect = 3.4
 Identities = 6/31 (19%), Positives = 10/31 (32%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G   L   N + A   A       +  D+ +
Sbjct: 16 GCRGLLPENTIAAFTKALLLGVTTLEFDLVI 46


>2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV,
           GRAM-positive bacteria, quinolone target, DNA binding,
           DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae}
           PDB: 3foe_A* 3fof_A*
          Length = 496

 Score = 25.4 bits (55), Expect = 3.7
 Identities = 7/26 (26%), Positives = 17/26 (65%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I+ +QL  ++  ++    +E++EL+E
Sbjct: 419 IVTLQLYRLTNTDVVVLQEEEAELRE 444


>1zcc_A Glycerophosphodiester phosphodiesterase; NYSGXRC, agrobacterium
          tumefaciens STR. C58, structural genomics, PSI; 2.50A
          {Agrobacterium tumefaciens str} SCOP: c.1.18.3
          Length = 248

 Score = 25.3 bits (54), Expect = 3.9
 Identities = 8/23 (34%), Positives = 12/23 (52%)

Query: 34 NGMEALELARQHKPDVIIMDIQL 56
          N   A +LA Q   D I +D++ 
Sbjct: 17 NTFAAADLALQQGADYIELDVRE 39


>3gfv_A Uncharacterized ABC transporter solute-binding protein YCLQ;
           alpha-beta-sandwich, periplasmic binding protein fold
           (PBP fold); 1.75A {Bacillus subtilis subsp}
          Length = 303

 Score = 25.3 bits (54), Expect = 4.0
 Identities = 8/41 (19%), Positives = 18/41 (43%)

Query: 40  ELARQHKPDVIIMDIQLQEISGLEITKQIKEDSELQEIPVI 80
           E   +  PD + +  +   I     TKQ+ E+  ++ +  +
Sbjct: 221 EYISKTNPDYLFVIDRGTAIGETSSTKQVVENDYVKNVNAV 261


>1vd6_A Glycerophosphoryl diester phosphodiesterase;
          glycerophosphodiester phosphodiesterase, glycerol
          complex; 1.30A {Thermus thermophilus HB8} SCOP:
          c.1.18.3 PDB: 1v8e_A
          Length = 224

 Score = 25.0 bits (53), Expect = 4.3
 Identities = 7/31 (22%), Positives = 13/31 (41%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G       N +E+  LA +   D + +D+  
Sbjct: 15 GAPLKAKENTLESFRLALEAGLDGVELDVWP 45


>3aek_B Light-independent protochlorophyllide reductase S; iron/sulfur
           cluster, oxidoreductase, bacteriochlorophyll
           biosynthesis; HET: PMR; 2.30A {Rhodobacter capsulatus}
           PDB: 3aeq_B* 3aer_B 3aes_B* 3aeu_B 3aet_B
          Length = 525

 Score = 25.1 bits (54), Expect = 4.6
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 5   VMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVII 51
           V +   N    +  R      G  AL T + +E  +      P++I+
Sbjct: 308 VGMGCYNREMARPLRTAAAEYGLEALITDDYLEVEKAIEAAAPELIL 354


>3l12_A Putative glycerophosphoryl diester phosphodiesterase; structural
          genomics, joint center for structural genomics, JCSG;
          HET: MSE; 1.60A {Silicibacter pomeroyi}
          Length = 313

 Score = 24.9 bits (53), Expect = 4.7
 Identities = 3/23 (13%), Positives = 7/23 (30%)

Query: 34 NGMEALELARQHKPDVIIMDIQL 56
          N +E            +  D+ +
Sbjct: 33 NTLEGFAFTLAAGVRALEFDVVM 55


>3i10_A Putative glycerophosphoryl diester phosphodiesterase;
          NP_812074.1, structural genomics; HET: MSE; 1.35A
          {Bacteroides thetaiotaomicron vpi-5482}
          Length = 278

 Score = 24.9 bits (53), Expect = 5.0
 Identities = 8/23 (34%), Positives = 13/23 (56%)

Query: 34 NGMEALELARQHKPDVIIMDIQL 56
          N   A++ A   K D++ +DIQ 
Sbjct: 33 NSTAAIDSAIAMKVDIVEIDIQK 55


>2wl2_A GYRA, DNA gyrase subunit A; isomerase, aminocoumarin antibiotic,
           drug target, protein-ligand complex; HET: DNA SM8; 2.62A
           {Escherichia coli} PDB: 1ab4_A 1x75_A*
          Length = 522

 Score = 24.9 bits (54), Expect = 5.0
 Identities = 11/26 (42%), Positives = 19/26 (73%)

Query: 51  IMDIQLQEISGLEITKQIKEDSELQE 76
           I+D++LQ+++GLE  K + E  EL +
Sbjct: 457 ILDLRLQKLTGLEHEKLLDEYKELLD 482


>2yyu_A Orotidine 5'-phosphate decarboxylase; TIM barrel, structural
          genomics, NPPSFA; HET: C5P; 2.20A {Geobacillus
          kaustophilus} PDB: 2yyt_A*
          Length = 246

 Score = 24.8 bits (53), Expect = 5.1
 Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 9/68 (13%)

Query: 27 YIALQTRNGMEALELARQHKPDVIIMDIQLQEIS--GLEITKQIKE-------DSELQEI 77
           +AL   +  E     R      + + + ++     G  I   +KE       D +L +I
Sbjct: 8  IVALDFPSKQEVERFLRPFAGTPLFVKVGMELYYQEGPAIVAFLKEQGHAVFLDLKLHDI 67

Query: 78 PVIAVTAF 85
          P     A 
Sbjct: 68 PNTVKQAM 75


>2o55_A Putative glycerophosphodiester phosphodiesterase; beta barrel,
          structural genomics, protein structure initiative,
          PSI-2; 2.81A {Galdieria sulphuraria}
          Length = 258

 Score = 25.0 bits (53), Expect = 5.1
 Identities = 4/23 (17%), Positives = 10/23 (43%)

Query: 34 NGMEALELARQHKPDVIIMDIQL 56
          N + +  L  +     I  D+++
Sbjct: 24 NTLRSFVLCMERNIPYIETDLRV 46


>2pz0_A Glycerophosphoryl diester phosphodiesterase;
          glycerophosphodiester phosphodiesterase, T.
          tengcongensis, hydrolase; 1.91A {Thermoanaerobacter
          tengcongensis MB4}
          Length = 252

 Score = 24.9 bits (53), Expect = 5.1
 Identities = 9/31 (29%), Positives = 14/31 (45%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G       N + A + A +   D I +D+QL
Sbjct: 19 GDSKNVPENTIAAFKRAMELGADGIELDVQL 49


>3ks6_A Glycerophosphoryl diester phosphodiesterase; structural genomics,
          joint center for structural genomics, JCSG; HET: MSE;
          1.80A {Agrobacterium tumefaciens str} PDB: 3ks5_A*
          Length = 250

 Score = 24.5 bits (52), Expect = 6.3
 Identities = 2/31 (6%), Positives = 6/31 (19%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G       +             + +  D+  
Sbjct: 10 GGTLEFGDSTPHGFTATAAMALEEVEFDLHP 40


>1o1z_A GDPD, glycerophosphodiester phosphodiesterase; TM1621,
          glycerophosphodiester phosphodiesterase (GDPD),
          structural genomics, JCSG, PSI; 1.60A {Thermotoga
          maritima} SCOP: c.1.18.3
          Length = 234

 Score = 24.5 bits (52), Expect = 6.4
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          GY A    N +EA   A +   + + +D++L
Sbjct: 20 GYSAKYLENTLEAFMKAIEAGANGVELDVRL 50


>3ldv_A Orotidine 5'-phosphate decarboxylase; structural genomics,
          infectious diseases; 1.77A {Vibrio cholerae o1 biovar
          el tor}
          Length = 255

 Score = 24.7 bits (53), Expect = 6.5
 Identities = 7/45 (15%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 28 IALQTRNGMEALELARQHKPDVIIMDIQLQEIS--GLEITKQIKE 70
          +AL   N  +AL    +  P    + +  +  +  G +  +++ +
Sbjct: 32 VALDYDNLADALAFVDKIDPSTCRLKVGKEMFTLFGPDFVRELHK 76


>1eix_A Orotidine 5'-monophosphate decarboxylase; alpha-beta-barrel,
          protein-inhibitor complex, homodimer, lyase; HET: BMQ;
          2.50A {Escherichia coli} SCOP: c.1.2.3 PDB: 1jjk_A*
          1l2u_A
          Length = 245

 Score = 24.6 bits (53), Expect = 6.6
 Identities = 7/45 (15%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 28 IALQTRNGMEALELARQHKPDVIIMDIQLQ--EISGLEITKQIKE 70
          +AL   N  +AL    +  P    + +  +   + G +  +++++
Sbjct: 19 VALDYHNRDDALAFVDKIDPRDCRLKVGKEMFTLFGPQFVRELQQ 63


>1ydy_A Glycerophosphoryl diester phosphodiesterase; structural genomics,
          PSI, protein structure initiative; 1.70A {Escherichia
          coli} SCOP: c.1.18.3 PDB: 1t8q_A
          Length = 356

 Score = 24.3 bits (51), Expect = 6.7
 Identities = 5/31 (16%), Positives = 11/31 (35%)

Query: 26 GYIALQTRNGMEALELARQHKPDVIIMDIQL 56
          G       + + A  +A     D +  D+ +
Sbjct: 38 GASGYLPEHTLPAKAMAYAQGADYLEQDLVM 68


>1s7i_A Hypothetical protein PA1349; structural genomics, protein structure
           initiative, MCSG, PSI, midwest center for structural
           genomics; 1.80A {Pseudomonas aeruginosa} SCOP: d.58.4.9
          Length = 124

 Score = 24.4 bits (53), Expect = 7.3
 Identities = 5/21 (23%), Positives = 13/21 (61%)

Query: 25  SGYIALQTRNGMEALELARQH 45
            G+  ++ R+  +AL++A + 
Sbjct: 85  GGFYLIEARDLNQALQIAAKI 105


>1q6o_A Humps, 3-keto-L-gulonate 6-phosphate decarboxylase, D-; beta
          barrel, lyase; HET: LG6; 1.20A {Escherichia coli} SCOP:
          c.1.2.3 PDB: 1kw1_A* 1q6l_A* 1kv8_A* 1q6q_A* 1q6r_A*
          1xbv_A* 1so5_A* 1so4_A* 1xby_A* 1so3_A* 1so6_A* 1xbz_A*
          1xbx_A*
          Length = 216

 Score = 24.3 bits (52), Expect = 7.7
 Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 2/74 (2%)

Query: 28 IALQTRNGMEALELARQHKPDVIIMDIQLQEI--SGLEITKQIKEDSELQEIPVIAVTAF 85
          +AL  +    A E  R    +V I+++        G+   + +K     + +   A  A 
Sbjct: 8  VALDNQTMDSAYETTRLIAEEVDIIEVGTILCVGEGVRAVRDLKALYPHKIVLADAKIAD 67

Query: 86 AMKGDEERIRKGGC 99
          A K       +   
Sbjct: 68 AGKILSRMCFEANA 81


>3gdh_A Trimethylguanosine synthase homolog; M7G, CAP, dimethyltransferase,
           usnRNA, snoRNA, telomerase, cytoplasm,
           methyltransferase, nucleus; HET: MGP SAH; 2.00A {Homo
           sapiens} PDB: 3egi_A*
          Length = 241

 Score = 24.3 bits (52), Expect = 8.0
 Identities = 11/51 (21%), Positives = 22/51 (43%)

Query: 3   KKVMIVEDNELNMKLFRDLIETSGYIALQTRNGMEALELARQHKPDVIIMD 53
            +V+ ++ + + + L R+  E  G          + L LA   K DV+ + 
Sbjct: 101 MRVIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLLLASFLKADVVFLS 151


>3fkq_A NTRC-like two-domain protein; RER070207001320, structural genomics,
           joint center for structural genomics, JCSG, protein
           structure initiative; HET: ATP 2PE; 2.10A {Eubacterium
           rectale}
          Length = 373

 Score = 24.4 bits (52), Expect = 8.1
 Identities = 18/125 (14%), Positives = 40/125 (32%), Gaps = 19/125 (15%)

Query: 1   MLKKVMIVEDNELNMKLFRDLIETSGYIALQTR---NGMEALELARQHKPDVIIMDIQLQ 57
           M  KV +++ ++  +     +  T     L+     +   A+E  ++++ DV+I +    
Sbjct: 20  MKIKVALLDKDKEYLDRLTGVFNTKYADKLEVYSFTDEKNAIESVKEYRIDVLIAE---- 75

Query: 58  EISGLEITKQIKEDSELQEIPVIAVTAFAMKGDEERIRKGGCEAYISKPISLSIFMETIK 117
                       ED  + +         A       I     E  I K   + +  + I 
Sbjct: 76  ------------EDFNIDKSEFKRNCGLAYFTGTPGIELIKDEIAICKYQRVDVIFKQIL 123

Query: 118 KYIGE 122
               +
Sbjct: 124 GVYSD 128


>1woj_A CNP, cnpase, 2',3'-cyclic-nucleotide 3'-phosphodiesterase;
           hydrolase; 1.80A {Homo sapiens} PDB: 2ilx_A
          Length = 214

 Score = 24.0 bits (52), Expect = 8.9
 Identities = 7/36 (19%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 85  FAMKGDEERIRKGGCEAYISKPISLSIFMETIKKYI 120
           F  K   E +RK G + ++ +  +   F + +++++
Sbjct: 8   FLTKKSSETLRKAG-QVFLEELGNHKAFKKELRQFV 42


>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail,
          transcription regulation, repressor, phosphorylation.;
          2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9
          Length = 289

 Score = 24.1 bits (52), Expect = 9.0
 Identities = 4/33 (12%), Positives = 13/33 (39%), Gaps = 4/33 (12%)

Query: 4  KVMIVE---DN-ELNMKLFRDLIETSGYIALQT 32
           + + +    N      + R L+    ++++ T
Sbjct: 13 YLFVRDVWKSNLYSEFAVIRQLVSQYNHVSIST 45


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.318    0.136    0.360 

Gapped
Lambda     K      H
   0.267   0.0754    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,036,536
Number of extensions: 46035
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 319
Number of HSP's successfully gapped: 163
Length of query: 123
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 42
Effective length of database: 3,729,466
Effective search space: 156637572
Effective search space used: 156637572
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: 51 (23.4 bits)