RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780892|ref|YP_003065305.1| probable two-component
response regulator protein [Candidatus Liberibacter asiaticus str.
psy62]
         (133 letters)



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

 Score = 63.4 bits (154), Expect = 2e-11
 Identities = 28/119 (23%), Positives = 52/119 (43%), Gaps = 2/119 (1%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDF--GFMVFEATSVCEAREFCEKELLPNYLVIDESMEG 58
           +  +L+VD  H++R   ++L      G  V  A +V +A  F E +   + +++D ++  
Sbjct: 3   LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNLPD 62

Query: 59  VLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
                  VR         V  +  E D E + A   AGA+ F+ K  + + L  A+  +
Sbjct: 63  AEAIDGLVRLKRFDPSNAVALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLI 121


>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 = 61.6 bits (150), Expect = 5e-11
 Identities = 28/117 (23%), Positives = 56/117 (47%), Gaps = 3/117 (2%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGF-MVFEATSVCEAREFCEKELLPNYLVIDESM--EGVL 60
           LL+VD S  +R++ ++  +  G+  V EA    EA E  +       L+ D +M     L
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTKVLITDWNMPEMNGL 67

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           + +  VR      ++ +  +  E    ++I   +AG N++++KPF  + L+  +  +
Sbjct: 68  DLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVV 124


>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 = 61.5 bits (149), Expect = 6e-11
 Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 3/115 (2%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEG--VLEF 62
           L+VD + + R+         G     A    EAR +   +     ++ D  M+    L+ 
Sbjct: 11  LVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQKRIGLMITDLRMQPESGLDL 70

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           I  +R       + +  +  + D E+ +     G   FLLKP +   L   + + 
Sbjct: 71  IRTIRASE-RAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKE 124


>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 = 60.2 bits (146), Expect = 1e-10
 Identities = 15/115 (13%), Positives = 40/115 (34%), Gaps = 3/115 (2%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LEF 62
           L+V+ + +  K+   L    G+   +      A     +   P+ +++D  +  +  LE 
Sbjct: 5   LIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIARENK-PDLILMDIQLPEISGLEV 63

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              +++      + V  +               G  +++ KP +       ++ L
Sbjct: 64  TKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRL 118


>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 = 59.7 bits (144), Expect = 2e-10
 Identities = 19/127 (14%), Positives = 45/127 (35%), Gaps = 12/127 (9%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCE--------KELLPNYLVI 52
           ++++++      ++        G    +   T    A  +                 +++
Sbjct: 6   TIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLL 65

Query: 53  DESMEG--VLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETL 110
           D ++     ++ +  V++ P      V  L    D  ++      GAN ++ KP N E  
Sbjct: 66  DLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENF 125

Query: 111 RFAMREL 117
             A+R+L
Sbjct: 126 ANAIRQL 132


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

 Score = 59.6 bits (145), Expect = 2e-10
 Identities = 19/122 (15%), Positives = 52/122 (42%), Gaps = 5/122 (4%)

Query: 1   MD-SLLLVDSSHIVRKVGRHLFNDFG-FMVFEATSVCEAREFCEKELLPNYLVIDESM-- 56
           +D ++LL+D     R+  + +F++ G +   E  ++ +     +       +++D +   
Sbjct: 3   LDGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLDSITLIIMDIAFPV 62

Query: 57  -EGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMR 115
            +  LE ++ +R      +  V       +     A  +   + ++LKP+  + L  ++R
Sbjct: 63  EKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVR 122

Query: 116 EL 117
            +
Sbjct: 123 SV 124


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

 Score = 59.6 bits (145), Expect = 2e-10
 Identities = 24/116 (20%), Positives = 48/116 (41%), Gaps = 4/116 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD    +      +     + V  A +  +A         P  + +D SM  +  L+
Sbjct: 9   ILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLSTFE-PAIMTLDLSMPKLDGLD 67

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            I  +RQ  +  +     ++  +D  K+      GA+ +L KPF+ + L   + +L
Sbjct: 68  VIRSLRQNKV-ANQPKILVVSGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDL 122


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

 Score = 59.2 bits (144), Expect = 3e-10
 Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 5/115 (4%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LEF 62
           L+V++S  +R+  R L +   F    A       +       P+ L+ D +M+G+     
Sbjct: 8   LIVENSWTMRETLRLLLSG-EFDCTTAADGASGLQQALAHP-PDVLISDVNMDGMDGYAL 65

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             H R  P    + V ++       +  A  +   +++L+KP     L   +  L
Sbjct: 66  CGHFRSEPTLKHIPVIFVSGYAPRTEGPAD-QPVPDAYLVKPVKPPVLIAQLHAL 119


>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 = 59.2 bits (143), Expect = 3e-10
 Identities = 17/129 (13%), Positives = 45/129 (34%), Gaps = 7/129 (5%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDF--GFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV- 59
           S+L+++       +      +      +  A +  +A +          +V+ + M    
Sbjct: 10  SILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTV--KPDVVMLDLMMVGM 67

Query: 60  --LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
                   ++  P   ++ V  +   +  + +      GA +   KP N   L   +++L
Sbjct: 68  DGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQL 127

Query: 118 PQMQKSKDE 126
            + +K+  E
Sbjct: 128 VEQKKATSE 136


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

 Score = 58.4 bits (141), Expect = 5e-10
 Identities = 17/119 (14%), Positives = 40/119 (33%), Gaps = 4/119 (3%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV- 59
           +   L+V+      +  + L    GF      S  +A          + + ID ++    
Sbjct: 3   LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRG-YDAVFIDLNLPDTS 61

Query: 60  -LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            L  +  +R +P+        +      +     A    + +L KP +  +L   ++ +
Sbjct: 62  GLALVKQLRALPMEKTSKFVAVSGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSI 119


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

 Score = 58.4 bits (141), Expect = 5e-10
 Identities = 23/130 (17%), Positives = 51/130 (39%), Gaps = 6/130 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +LLVDS  ++ +  + L +   + +  A    +A +        + ++    +  +    
Sbjct: 17  ILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLASRE-VDLVISAAHLPQMDGPT 75

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGA-NSFLLKPFNRETLRFAMRELPQM 120
            +A + Q           L  + D + +      G    +L KP++ + L  A+R+  + 
Sbjct: 76  LLARIHQQ--YPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQALEH 133

Query: 121 QKSKDENQFL 130
           Q S+ E   L
Sbjct: 134 QHSERERLRL 143


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

 Score = 58.5 bits (141), Expect = 5e-10
 Identities = 17/116 (14%), Positives = 39/116 (33%), Gaps = 1/116 (0%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLV-IDESMEGVLE 61
           S+L+ + + I R V           +   T+  +A +  +       ++ I   +   LE
Sbjct: 12  SVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQNRQFDVIIMDIQMPVMDGLE 71

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            ++ +R      +     ++             A  + ++ KP N   LR  +   
Sbjct: 72  AVSEIRNYERTHNTKRASIIAITADTIDDDRPGAELDEYVSKPLNPNQLRDVVLTC 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 = 58.4 bits (141), Expect = 5e-10
 Identities = 29/130 (22%), Positives = 50/130 (38%), Gaps = 5/130 (3%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--L 60
           S+ L+D    +RK  +      GF V    S  EA      +     ++ D  M G+  L
Sbjct: 5   SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADF-AGIVISDIRMPGMDGL 63

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQM 120
                +    L  D+ +  +    D    +   + GA  F+ KPF  + L  + R   + 
Sbjct: 64  ALFRKILA--LDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEK 121

Query: 121 QKSKDENQFL 130
           ++   EN+ L
Sbjct: 122 RRLVMENRSL 131


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

 Score = 58.0 bits (140), Expect = 7e-10
 Identities = 24/126 (19%), Positives = 55/126 (43%), Gaps = 7/126 (5%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEG 58
           + SL++ +  +++R+    L    G    + +  +  +A +  E E  PN +++D  M G
Sbjct: 3   LTSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIE-EYNPNVVILDIEMPG 61

Query: 59  V--LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRE 116
           +  LE +A +R+  L   V +  +                 ++++LK  + E L   + +
Sbjct: 62  MTGLEVLAEIRKKHLNIKVII--VTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINK 119

Query: 117 LPQMQK 122
           +   +K
Sbjct: 120 VNNGEK 125


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

 Score = 57.7 bits (140), Expect = 7e-10
 Identities = 28/118 (23%), Positives = 48/118 (40%), Gaps = 5/118 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+ D     R V + L    G  V       +  +   +E   + +++D  M G+  L+
Sbjct: 17  MLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMAEED-YDAVIVDLHMPGMNGLD 75

Query: 62  FIAHVRQM--PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            +  +R M         V  L  +V  E + A  +AGA +FL KP     L   + +L
Sbjct: 76  MLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADL 133


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

 Score = 57.4 bits (138), Expect = 1e-09
 Identities = 15/117 (12%), Positives = 41/117 (35%), Gaps = 4/117 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEG--VLE 61
           +L+ +    + ++   +    GF      S  +A E   +      + +D ++     + 
Sbjct: 9   ILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRP-YAAMTVDLNLPDQDGVS 67

Query: 62  FIAHVRQMPLGTDVFVYYLLMEV-DFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            I  +R+     D+ +  +     + E          +++L KP +   L  ++   
Sbjct: 68  LIRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRA 124


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

 Score = 57.4 bits (138), Expect = 1e-09
 Identities = 22/131 (16%), Positives = 46/131 (35%), Gaps = 5/131 (3%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKE----LLPNYLVIDESM 56
           + ++++VD +  V    + L  +    V   +S         +E    +L +        
Sbjct: 3   LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGIN 62

Query: 57  EGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRE 116
            G               D+ V       D +  + G + GA+ F++KP++ + L   +  
Sbjct: 63  NGNEGLFWLHEIKRQYRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLN 122

Query: 117 -LPQMQKSKDE 126
              Q +  K E
Sbjct: 123 AASQAKDGKKE 133


>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 = 56.7 bits (136), Expect = 1e-09
 Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 3/131 (2%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD      ++         + V  A     A     ++L P+ +++D  M G+    
Sbjct: 4   ILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDL-PDIILLDVMMPGMDGFT 62

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQ 121
               ++  P    + V  +         I G  +GA+ FL KP +   L   +R L + +
Sbjct: 63  VCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFK 122

Query: 122 KSKDENQFLDA 132
              DE +  +A
Sbjct: 123 LVIDELRQREA 133


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

 Score = 56.6 bits (136), Expect = 2e-09
 Identities = 22/124 (17%), Positives = 49/124 (39%), Gaps = 10/124 (8%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKE------LLPNYLVIDES 55
           +LLV+ S    ++ + +         +        A  F +++        PN +++D +
Sbjct: 11  ILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLN 70

Query: 56  MEGV--LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFA 113
           +      E +A ++Q P    + V  L    + + +IA      N +L K  N + L   
Sbjct: 71  LPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKM 130

Query: 114 MREL 117
           ++ +
Sbjct: 131 VQGI 134


>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 = 56.8 bits (137), Expect = 2e-09
 Identities = 27/118 (22%), Positives = 48/118 (40%), Gaps = 7/118 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV-- 59
           +++ D   + R+      +  G +  V EA     A E  +   LP+  ++D  M G+  
Sbjct: 18  VVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIK-AHLPDVALLDYRMPGMDG 76

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            +  A VR   L T V +  +    +   +    + GA  FLLK   R  +  A+ + 
Sbjct: 77  AQVAAAVRSYELPTRVLL--ISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDC 132


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

 Score = 56.1 bits (135), Expect = 2e-09
 Identities = 19/117 (16%), Positives = 39/117 (33%), Gaps = 3/117 (2%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L++D + + R V + L    G  V   +S  E       E    ++ +        +  
Sbjct: 10  VLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVSHEHKVVFMDVCMPGVENYQIA 69

Query: 64  AHVRQM---PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             + +           +  L    D          G +  LLKP + + +R  + +L
Sbjct: 70  LRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDL 126


>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 = 56.3 bits (135), Expect = 2e-09
 Identities = 21/125 (16%), Positives = 46/125 (36%), Gaps = 5/125 (4%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LEF 62
           L+VD   I R++        G+    A    +A     K    + ++ D +M  +     
Sbjct: 133 LVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLSKNH-IDIVLSDVNMPNMDGYRL 191

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQK 122
              +RQ+  G  + V  +      E+      +G +S L KP   + ++  +    +  +
Sbjct: 192 TQRIRQL--GLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVR 249

Query: 123 SKDEN 127
              ++
Sbjct: 250 KSRDS 254


>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 = 56.3 bits (136), Expect = 2e-09
 Identities = 31/117 (26%), Positives = 58/117 (49%), Gaps = 4/117 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGF-MVFEATSVCEAREFCEKELLPNYLVIDESMEGV--L 60
            L+VD    +R++ R+L  + GF  V EA    +A    +      +++ D +M  +  L
Sbjct: 7   FLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGG-YGFVISDWNMPNMDGL 65

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           E +  +R     + + V  +  E   E +IA A+AGA+ +++KPF   TL   + ++
Sbjct: 66  ELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 122


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

 Score = 56.0 bits (135), Expect = 2e-09
 Identities = 21/124 (16%), Positives = 46/124 (37%), Gaps = 5/124 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+V+     R+    + ++    V+ A    E          P+ ++ D  M  +  LE
Sbjct: 10  ILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHA-PDVIITDIRMPKLGGLE 68

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQ 121
            +  ++       V V  +    + +  I     G + FL KP     L   + +   ++
Sbjct: 69  MLDRIKAGGAKPYVIV--ISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIK 126

Query: 122 KSKD 125
            +K+
Sbjct: 127 LAKE 130


>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 = 55.9 bits (134), Expect = 3e-09
 Identities = 22/125 (17%), Positives = 46/125 (36%), Gaps = 1/125 (0%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLP-NYLVIDESMEGVLEFI 63
           ++VD    VR   + + +D GF +  A S  +  +  +K       L I        + I
Sbjct: 11  MIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTI 70

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQKS 123
             +    L   + +  L  +   +  + G +     ++ KPF+ E L           ++
Sbjct: 71  RAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVRN 130

Query: 124 KDENQ 128
           +  N+
Sbjct: 131 QTGNE 135


>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 = 55.2 bits (133), Expect = 4e-09
 Identities = 16/116 (13%), Positives = 41/116 (35%), Gaps = 5/116 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV-- 59
           +++VD + ++R               V +A +  EA +    +   + +++D  M  +  
Sbjct: 16  VMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMDG 75

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMR 115
           +EF+ H +       + +   +              GA+  + KP    +     +
Sbjct: 76  MEFLRHAKLKT-RAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTVSHDLEEK 130


>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 = 55.2 bits (132), Expect = 5e-09
 Identities = 21/129 (16%), Positives = 43/129 (33%), Gaps = 1/129 (0%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATS-VCEAREFCEKELLPNYLVIDESMEGV 59
           + ++L+VD S ++  V   +    G+    A S                 L I       
Sbjct: 3   LYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDG 62

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQ 119
            E +  ++  P   D+ V  L  +    +      +    ++LKP     L  A+  +  
Sbjct: 63  WETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVLA 122

Query: 120 MQKSKDENQ 128
            + S   ++
Sbjct: 123 RRHSIAADE 131


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

 Score = 55.1 bits (132), Expect = 5e-09
 Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 2/115 (1%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           ++++VD S I     ++     GF V  A +  EA  F  +E +    V     E  L  
Sbjct: 6   TVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLRREKIDLVFVDVFEGEESLNL 65

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           I  +R+     D  V  L   VD + +I   +AGA  ++LKPF  + L   ++++
Sbjct: 66  IRRIREE--FPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKI 118


>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 = 54.9 bits (132), Expect = 6e-09
 Identities = 19/113 (16%), Positives = 37/113 (32%), Gaps = 1/113 (0%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFIA 64
            +VD    +R V        G       +  E       +  P+ L+ D  M G+     
Sbjct: 7   WVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKT-PDVLLSDIRMPGMDGLAL 65

Query: 65  HVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             +       + V  +    D +  ++  + GA  +L KPF+ +     +   
Sbjct: 66  LKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA 118


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

 Score = 54.7 bits (131), Expect = 7e-09
 Identities = 18/120 (15%), Positives = 39/120 (32%), Gaps = 6/120 (5%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGF-MVFEATSVCEAREFCEKELLPNYLVIDESMEGV 59
           +  +L+V+   +     R      G+ ++    +  EA            LV       +
Sbjct: 9   LPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGAL 68

Query: 60  --LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             +E  A +       ++ + ++    D E      R     +L KP   +TL  ++   
Sbjct: 69  DGVETAARLAAGC---NLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMA 125


>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 = 54.7 bits (131), Expect = 7e-09
 Identities = 20/117 (17%), Positives = 42/117 (35%), Gaps = 5/117 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESM---EGVL 60
           ++LVD+            +  GF + +  +  EA     K     +L+I E+       +
Sbjct: 11  IMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKT--HPHLIITEANMPKISGM 68

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           +    +++ P    + V  L      ++       G   F+ KP N   L   ++ +
Sbjct: 69  DLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRV 125


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

 Score = 54.4 bits (131), Expect = 9e-09
 Identities = 23/116 (19%), Positives = 46/116 (39%), Gaps = 6/116 (5%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVF-EATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +++D   +     R+L       +  E T    A +  E  L P+ ++ID  + GV  ++
Sbjct: 5   IIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE-TLKPDIVIIDVDIPGVNGIQ 63

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            +  +R+      + +  +  + D       A AGAN F+ K      +  A+   
Sbjct: 64  VLETLRKRQYSGIIII--VSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAA 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 = 54.2 bits (130), Expect = 1e-08
 Identities = 18/127 (14%), Positives = 49/127 (38%), Gaps = 13/127 (10%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKE---------LLPNYLVI 52
           LL+V+ S       + L    G +  ++   +  +A +F  +            P  +++
Sbjct: 9   LLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILL 68

Query: 53  DESMEGV--LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETL 110
           D ++ G    E +  ++Q  +   + V  +    + + +        +S+++KP   + L
Sbjct: 69  DLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRL 128

Query: 111 RFAMREL 117
              ++  
Sbjct: 129 TETVQTF 135


>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 = 54.1 bits (130), Expect = 1e-08
 Identities = 22/118 (18%), Positives = 47/118 (39%), Gaps = 6/118 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV-- 59
           + + D +  +  +     +    M  +  A +  +  +  E++  P+ L++D  M  +  
Sbjct: 5   VCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKR-PDILLLDIIMPHLDG 63

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           L  +  +R         V  L      +        GA+ F+LKPF+ E L   +R++
Sbjct: 64  LAVLERIRAGF-EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQV 120


>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 = 53.4 bits (129), Expect = 2e-08
 Identities = 24/115 (20%), Positives = 46/115 (40%), Gaps = 6/115 (5%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LEF 62
           L+VD    +  +        G+ V  A    EA E  E+   P+ +++D  +     +E 
Sbjct: 6   LVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQ-PDLILLDIMLPNKDGVEV 64

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              VR+     D+ +  L  +      + G   GA+ ++ KPF+   L   ++  
Sbjct: 65  CREVRKKY---DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKAN 116


>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 = 53.4 bits (128), Expect = 2e-08
 Identities = 16/123 (13%), Positives = 43/123 (34%), Gaps = 10/123 (8%)

Query: 5   LLVDSSHIVRKVGRHLFND--FGFMVFEATSVCEAREFCEKE------LLPNYLVIDESM 56
            LV+ +    ++ +    +      V       EA  +  +E        P+ +++  ++
Sbjct: 6   FLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNL 65

Query: 57  EGV--LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAM 114
                 E +A ++  P    + V  L   ++ + +        N ++ K  N   L   +
Sbjct: 66  PKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIV 125

Query: 115 REL 117
           + +
Sbjct: 126 KGI 128


>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 = 53.2 bits (127), Expect = 2e-08
 Identities = 26/131 (19%), Positives = 51/131 (38%), Gaps = 1/131 (0%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           +  +L++D    + +  + L    G  V  A+S  E      +      +VI +     L
Sbjct: 3   LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKL 62

Query: 61  EFIAHVRQMP-LGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQ 119
             +  +R++  +   + V  L    D +  I   + GA  +L KP   + L  A+     
Sbjct: 63  SGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAIN 122

Query: 120 MQKSKDENQFL 130
            +K   EN+ +
Sbjct: 123 RKKLLMENERM 133


>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 = 53.0 bits (127), Expect = 2e-08
 Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 4/116 (3%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFM-VFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           L+VD     R +        GF  +  A    +  +   +    + ++ D +M  +  L 
Sbjct: 10  LIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNP-HHLVISDFNMPKMDGLG 68

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            +  VR  P         L  + D   +   A  GAN+ L KPF  E ++ A+  +
Sbjct: 69  LLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAV 124


>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 = 52.9 bits (127), Expect = 2e-08
 Identities = 24/116 (20%), Positives = 57/116 (49%), Gaps = 5/116 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD    +R +   +FN  G+  F+A +  +A +   KE  P+ +++D  + G+  +E
Sbjct: 6   ILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVTKER-PDLVLLDMKIPGMDGIE 64

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            +  ++ +     V +  +    + + +      GA +   KPF+ + +R A+++ 
Sbjct: 65  ILKRMKVIDENIRVII--MTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKY 118


>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 = 52.7 bits (126), Expect = 3e-08
 Identities = 24/115 (20%), Positives = 42/115 (36%), Gaps = 1/115 (0%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLP-NYLVIDESMEGVLEF 62
           +LLVD S ++RK+        G+ V EA +   A E   +       L I   +      
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTV 64

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           +  +++      + V  L  +   E        GA   + KPF+       ++ L
Sbjct: 65  LKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHL 119


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

 Score = 52.3 bits (125), Expect = 3e-08
 Identities = 33/133 (24%), Positives = 55/133 (41%), Gaps = 6/133 (4%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV- 59
             +LL++D   +VR+       D  F V +A +  +  +  E E  P+ ++ D  M  + 
Sbjct: 5   SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFESEQ-PDLVICDLRMPQID 63

Query: 60  -LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKP-FNRETLRFAMREL 117
            LE I  +RQ    T + V  L         +   R GA  +L+KP  +   L  ++R  
Sbjct: 64  GLELIRRIRQTASETPIIV--LSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRA 121

Query: 118 PQMQKSKDENQFL 130
                 + ENQ  
Sbjct: 122 LDRAYLRVENQRY 134


>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 = 52.5 bits (125), Expect = 3e-08
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 2/114 (1%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L+V+   + R   + +F   G+ VFEAT   E  +   +      LVI +        +
Sbjct: 6   ILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEY--DINLVIMDINLPGKNGL 63

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              R++    +V + +L    +    I G   GA+ ++ KPFN   L    R L
Sbjct: 64  LLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL 117


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

 Score = 52.3 bits (125), Expect = 3e-08
 Identities = 15/120 (12%), Positives = 34/120 (28%), Gaps = 3/120 (2%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           ++ + +VD   +   + + +       V               +     L +       +
Sbjct: 3   LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLSLNKQDIIILDLMMPDMDGI 62

Query: 61  EFIAHVRQMPLGTDVFV---YYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           E I H+ +      + +   Y   +    E +         +   KP N E L   +  L
Sbjct: 63  EVIRHLAEHKSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSL 122


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

 Score = 52.2 bits (125), Expect = 4e-08
 Identities = 24/116 (20%), Positives = 47/116 (40%), Gaps = 6/116 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD    +  +        G+ V  A    EA E  E+   P+ +++D  +     +E
Sbjct: 5   ILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQ-PDLILLDIMLPNKDGVE 63

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
               VR+     D+ +  L  +      + G   GA+ ++ KPF+   L   ++  
Sbjct: 64  VCREVRKKY---DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKAN 116


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

 Score = 52.0 bits (124), Expect = 4e-08
 Identities = 17/124 (13%), Positives = 49/124 (39%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L+V+ S    K   ++ N +G+ V  A +   A E       P+ +++D  +   ++ +
Sbjct: 8   ILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGV 67

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQKS 123
                +   +++ V +L    +   +       A  +++K    + L   +    ++ ++
Sbjct: 68  QTALAIQQISELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEA 127

Query: 124 KDEN 127
               
Sbjct: 128 NVHA 131


>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 = 52.1 bits (124), Expect = 5e-08
 Identities = 20/117 (17%), Positives = 42/117 (35%), Gaps = 1/117 (0%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           +  +L+VD    +    + +    G+ V  A +  E     E E   N  +    +  + 
Sbjct: 3   LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEF-FNLALFXIKLPDME 61

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
                 +   L   +    +      E  +    AGA+++++KP N   L   ++E 
Sbjct: 62  GTELLEKAHKLRPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEK 118


>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 = 51.9 bits (124), Expect = 5e-08
 Identities = 20/116 (17%), Positives = 42/116 (36%), Gaps = 2/116 (1%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGF-MVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           +L+VD S    K    +F   GF ++  A    EA    +       +V        ++ 
Sbjct: 39  VLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDG 98

Query: 63  IAHVRQM-PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           I  +  +     +  V  +      + +      GA +F++KP +R  +   +  +
Sbjct: 99  ITCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSV 154


>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 = 51.6 bits (123), Expect = 5e-08
 Identities = 21/126 (16%), Positives = 44/126 (34%), Gaps = 2/126 (1%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           S+L+V+    +      L    GF     T    A    ++      +V+ + M   +  
Sbjct: 6   SVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFDRA--GADIVLLDLMLPGMSG 63

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQK 122
               +Q+   + V V  +         + G   GA+ ++ KP++   L   +R + +   
Sbjct: 64  TDVCKQLRARSSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRGG 123

Query: 123 SKDENQ 128
             D   
Sbjct: 124 DDDSEM 129


>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 = 51.5 bits (123), Expect = 5e-08
 Identities = 24/117 (20%), Positives = 50/117 (42%), Gaps = 2/117 (1%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           M  +L+VD    +  + +      G+ V  A +  EA E  E E     ++I + M   +
Sbjct: 1   MKKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAE--QPDIIILDLMLPEI 58

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           + +   + +   + V +  L  +      + G   GA+ ++ KPF+   L+  ++ L
Sbjct: 59  DGLEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKAL 115


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

 Score = 51.2 bits (122), Expect = 7e-08
 Identities = 25/129 (19%), Positives = 49/129 (37%), Gaps = 2/129 (1%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           +++LVD    +    + L    G  +   TS  +A E  +       ++ D  M  +   
Sbjct: 9   TVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTS-VQLVISDMRMPEMGGE 67

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGA-NSFLLKPFNRETLRFAMRELPQMQ 121
           +   +      D+    +    D +  I     G  + FLLKP+  E +   + +  Q+ 
Sbjct: 68  VFLEQVAKSYPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQLA 127

Query: 122 KSKDENQFL 130
             ++EN  L
Sbjct: 128 FLREENLRL 136


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

 Score = 51.1 bits (122), Expect = 8e-08
 Identities = 26/132 (19%), Positives = 52/132 (39%), Gaps = 12/132 (9%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMV---FEATSVCEAREFCEKELLPNYLVIDESMEGV- 59
           +L+VD   + R       N          +A     A +   K   PN L+ D  M  + 
Sbjct: 5   ILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIALKHP-PNVLLTDVRMPRMD 63

Query: 60  -LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETL----RFAM 114
            +E + ++ +  L  D  V ++    D E + A  +  A  ++ KP +   +    + ++
Sbjct: 64  GIELVDNILK--LYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSI 121

Query: 115 RELPQMQKSKDE 126
           + + Q Q  +D 
Sbjct: 122 QTVLQHQAQQDS 133


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

 Score = 50.8 bits (121), Expect = 9e-08
 Identities = 16/114 (14%), Positives = 31/114 (27%), Gaps = 1/114 (0%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLV-IDESMEGVLEFI 63
            LVD     R     L +     +    S          +     ++      +      
Sbjct: 10  YLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSGIE 69

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
                +  G  +    +    D    +   RA A  F+ KPF    L   ++++
Sbjct: 70  LLETLVKRGFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQI 123


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

 Score = 50.9 bits (121), Expect = 9e-08
 Identities = 19/125 (15%), Positives = 48/125 (38%), Gaps = 2/125 (1%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L++D      +  +    + G  +  A +  EA            L+  E +    +  
Sbjct: 7   ILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYD--LIFLEIILSDGDGW 64

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQKS 123
              +++   T   + Y+    + + ++    +G + +L+KP N E L   ++ + +   S
Sbjct: 65  TLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 124

Query: 124 KDENQ 128
              N+
Sbjct: 125 YVNNE 129


>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 = 50.8 bits (121), Expect = 9e-08
 Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 2/117 (1%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           M ++L+V+    +R+  R      G  VFEA ++               L+I +      
Sbjct: 1   MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATR--KPDLIILDLGLPDG 58

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           + I  +R +   + V V  L    +    IA   AGA+ +L KPF    L+  +R  
Sbjct: 59  DGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVA 115


>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 = 50.8 bits (121), Expect = 9e-08
 Identities = 24/121 (19%), Positives = 44/121 (36%), Gaps = 8/121 (6%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPN-------YLVIDESM 56
           +L+V+ +H+ ++V + + N  G    E     +      KEL          ++ +    
Sbjct: 5   ILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPK 64

Query: 57  EGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRE 116
              L     +R+   G    +  L    D   +     +G N FL KP  R  L+  + E
Sbjct: 65  VDGLLSTKMIRRDL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTE 123

Query: 117 L 117
            
Sbjct: 124 F 124


>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 = 50.7 bits (121), Expect = 1e-07
 Identities = 24/127 (18%), Positives = 57/127 (44%), Gaps = 5/127 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD    +  + ++     G+ V  A+   EA +  E E  P+ +V+D  +  +  +E
Sbjct: 6   ILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEK-PDLIVLDVMLPKLDGIE 64

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQ 121
               +RQ  L   + +  L  + +    + G   GA+ ++ KPF+   +   ++ + +  
Sbjct: 65  VCKQLRQQKLMFPILM--LTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRS 122

Query: 122 KSKDENQ 128
           + +  + 
Sbjct: 123 EIRAPSS 129


>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 = 50.8 bits (121), Expect = 1e-07
 Identities = 24/116 (20%), Positives = 41/116 (35%), Gaps = 3/116 (2%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           ++LL D   I+         D GF+V   +S  +A E  +     + +V D       + 
Sbjct: 7   TILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDG 66

Query: 63  IAHVRQM-PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
               R    +  ++ + Y+      E    G        L KPF    L  A+ +L
Sbjct: 67  WQVARVAREIDPNMPIVYISGHAALEWASNGVPDSI--ILEKPFTSAQLITAVSQL 120


>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 = 50.5 bits (120), Expect = 1e-07
 Identities = 22/114 (19%), Positives = 48/114 (42%), Gaps = 1/114 (0%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L+V+ + ++R   +    D G  V +A    EA  +  + + P+  ++D  +       
Sbjct: 3   VLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHI-PDIAIVDLGLPDEDGLS 61

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              R       + +  L     ++  +    AGA+ ++ KPF+ E +   M+ L
Sbjct: 62  LIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL 115


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

 Score = 50.3 bits (120), Expect = 1e-07
 Identities = 14/126 (11%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV--L 60
           ++V+   + ++    L N    M  V       +  +F +     + + +D ++  +  +
Sbjct: 13  IIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQHNK-VDAIFLDINIPSLDGV 71

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQM 120
               ++ Q      +    + +    E  +      A  ++LKP+    +   +++L   
Sbjct: 72  LLAQNISQFAHKPFI----VFITAWKEHAVEAFELEAFDYILKPYQESRIINMLQKLTTA 127

Query: 121 QKSKDE 126
            + ++ 
Sbjct: 128 WEQQNN 133


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

 Score = 49.3 bits (117), Expect = 2e-07
 Identities = 18/116 (15%), Positives = 41/116 (35%), Gaps = 6/116 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +LL++       V   +    GF V        A +  +    P  +++         L 
Sbjct: 4   ILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLDLLQ-PIVILMAWPPPDQSCLL 62

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            + H+R+        +   ++ +    +     A A++ L KP + + L   ++ L
Sbjct: 63  LLQHLREHQADPHPPL---VLFLGEPPVDPLLTAQASAILSKPLDPQLLLTTLQGL 115


>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 = 49.1 bits (117), Expect = 3e-07
 Identities = 22/116 (18%), Positives = 51/116 (43%), Gaps = 4/116 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD +  +R + + +    G+ V    +         KEL P+ + +D +M  +  ++
Sbjct: 5   VLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGID 64

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
            I  + ++    +  +           +I   +AGA  F++KPF    +  A+ ++
Sbjct: 65  AIKEIMKI--DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118


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

 Score = 48.8 bits (116), Expect = 4e-07
 Identities = 31/132 (23%), Positives = 51/132 (38%), Gaps = 9/132 (6%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESM---EGV 59
           ++LLVD         +    D  F V  A     A    E+E     ++I +        
Sbjct: 3   AILLVDDEPHSLAAMKLALED-DFDVLTAQGAEAAIAILEEE--WVQVIICDQRMPGRTG 59

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGAR-AGANSFLLKPFNRETLRFAMRELP 118
           ++F+  VR+     +     +    D   M+A    AG + FL KP++ E L  + R   
Sbjct: 60  VDFLTEVRER--WPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAA 117

Query: 119 QMQKSKDENQFL 130
           +M     EN+ L
Sbjct: 118 RMFTLARENERL 129


>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 = 48.7 bits (116), Expect = 4e-07
 Identities = 24/132 (18%), Positives = 49/132 (37%), Gaps = 5/132 (3%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+VD    +      +  + G+    A ++ EA +  ++      +V+D  M     + 
Sbjct: 3   VLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKEL-FFPVIVLDVWMPDGDGVN 61

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQ 121
           FI  +++     D  V  +      +  +   + GA  FL KPF+ E     ++   +  
Sbjct: 62  FIDFIKEN--SPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEY 119

Query: 122 KSKDENQFLDAI 133
             K   Q     
Sbjct: 120 SKKAPPQEEIEF 131


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

 Score = 48.9 bits (116), Expect = 4e-07
 Identities = 21/126 (16%), Positives = 41/126 (32%), Gaps = 2/126 (1%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +LLVD  + +    +   +   F V    S  EA    +K    + +++D  M G+    
Sbjct: 7   ILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTE 65

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAG-ANSFLLKPFNRETLRFAMRELPQMQK 122
              +   +  +     L    D    +     G    FL KP     ++ A+    +   
Sbjct: 66  VIQKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQYD 125

Query: 123 SKDENQ 128
                +
Sbjct: 126 LVTSKE 131


>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 = 48.4 bits (115), Expect = 5e-07
 Identities = 24/115 (20%), Positives = 47/115 (40%), Gaps = 1/115 (0%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPN-YLVIDESMEGVLEF 62
           +L+V+    +R++   +    GF   EA     A     +       L         ++F
Sbjct: 5   ILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQF 64

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           I H+R+  +  D+ V  L    + E  + G   GA+  + KPF+ + L   ++ +
Sbjct: 65  IKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAV 119


>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 = 48.3 bits (115), Expect = 5e-07
 Identities = 19/110 (17%), Positives = 40/110 (36%), Gaps = 9/110 (8%)

Query: 4   LLLVDSSHIVRKVGRHLF--NDFGFMVFEATSVCEAREFCEKELLPNYLVIDE----SME 57
           +L+V+ +     + R +    D    +    +  +A    ++      L+I +       
Sbjct: 8   VLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQA--KYDLIILDIGLPIAN 65

Query: 58  GVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNR 107
           G  E ++ VR+        +  L   V  ++      AGA+S + K  N 
Sbjct: 66  G-FEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNN 114


>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 = 48.1 bits (114), Expect = 6e-07
 Identities = 18/116 (15%), Positives = 42/116 (36%), Gaps = 3/116 (2%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESM--EGVLE 61
           +L+V+S   +    R      GF V E T    + E   ++     ++  +    +    
Sbjct: 8   ILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYL 67

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
               +++     +V +  ++   D        +A A+ ++ KP + + L      L
Sbjct: 68  ICGKLKKDDDLKNVPIV-IIGNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGAL 122


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

 Score = 48.3 bits (114), Expect = 6e-07
 Identities = 23/130 (17%), Positives = 45/130 (34%), Gaps = 1/130 (0%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEG-VLEFI 63
           L+V+ S    +  +H+  + G+      +  EA  F         +      E       
Sbjct: 11  LIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALC 70

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQKS 123
             ++  P    + V  L +  D   ++     GA+ F+ KP     L   ++ L    K 
Sbjct: 71  RWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVKR 130

Query: 124 KDENQFLDAI 133
            +E    ++I
Sbjct: 131 TEERYSRESI 140


>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 = 47.4 bits (112), Expect = 1e-06
 Identities = 27/107 (25%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 5   LLVDSSHIVRK-VGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           LLVD   ++ + V R L ++ G      +   +A     +   P  ++ D  M GV  L 
Sbjct: 22  LLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVANQIK-PTVILQDLVMPGVDGLT 80

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRE 108
            +A  R  P   D+ +  L  + +     A   AGAN +L+K  +  
Sbjct: 81  LLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAI 127


>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 = 47.3 bits (112), Expect = 1e-06
 Identities = 22/114 (19%), Positives = 42/114 (36%), Gaps = 3/114 (2%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEF 62
           ++ +VD    VRK    +    GF V    S      F       N +++ +     +  
Sbjct: 5   TVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDV--RNGVLVTDLRMPDMSG 62

Query: 63  IAHVRQM-PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMR 115
           +  +R +  L  ++    +    D    +   +AGA  F+ KPF    +  A+ 
Sbjct: 63  VELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIE 116


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

 Score = 47.3 bits (112), Expect = 1e-06
 Identities = 22/120 (18%), Positives = 49/120 (40%), Gaps = 9/120 (7%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV- 59
           M  +L+VD    +R++ +    + G+ +  A +  EA +          LVI +      
Sbjct: 1   MKRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFFSG--NYDLVILDIEMPGI 58

Query: 60  --LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             LE    +R+      +    +L+          +   A+ +++K FN + L+  +++L
Sbjct: 59  SGLEVAGEIRKKKKDAKI----ILLTAYSHYRSDMSSWAADEYVVKSFNFDELKEKVKKL 114


>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 = 47.2 bits (112), Expect = 1e-06
 Identities = 26/128 (20%), Positives = 54/128 (42%), Gaps = 5/128 (3%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LEF 62
           L+++   + R +     +  G  V  A    EA +   ++   N +++D  +  V  LE 
Sbjct: 4   LVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEK-HFNVVLLDLLLPDVNGLEI 62

Query: 63  IAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQK 122
           +  +++    T+V V         +  +   + GA  FL KP   E +   + +  + +K
Sbjct: 63  LKWIKERSPETEVIVITGHG--TIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRK 120

Query: 123 SKDENQFL 130
            + EN+ L
Sbjct: 121 LRKENELL 128


>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 = 47.1 bits (111), Expect = 1e-06
 Identities = 19/114 (16%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +++V+   + +   +  F   G+ V    S    RE  + + +   L++ +        +
Sbjct: 5   IVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVD--LILLDINLPDENGL 62

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              R +   + V +  +    D    I G   GA+ ++ KP     L   ++ L
Sbjct: 63  MLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNL 116


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

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 18/117 (15%), Positives = 43/117 (36%), Gaps = 9/117 (7%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFG--FMVFEATSVCE-----AREFCEKELLPNYLVIDES 55
            +L ++   +  +    +F+       +  A S  +          E ++ P  +++D +
Sbjct: 9   DILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLDIN 68

Query: 56  MEG--VLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETL 110
           +     +EF+  +R     TD+ V+ L      +  +A         L+KP +    
Sbjct: 69  IPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEA 125


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

 Score = 46.0 bits (108), Expect = 3e-06
 Identities = 19/128 (14%), Positives = 41/128 (32%), Gaps = 11/128 (8%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNY---LVIDES 55
           +DS+LL+D   IV  +   +      +  +   TS   A     +         ++  + 
Sbjct: 9   IDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYAAGRWPSIICIDI 68

Query: 56  MEGVLEFIAHVRQM-----PLGTDVFVYYLLMEVD-FEKMIAGARAGANSFLLKPFNRET 109
               +     +        P+     V  L   +D  ++  A A    + ++ KP     
Sbjct: 69  NMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANA 128

Query: 110 LRFAMREL 117
           L     ++
Sbjct: 129 LNNLYNKV 136


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

 Score = 45.9 bits (108), Expect = 3e-06
 Identities = 22/123 (17%), Positives = 47/123 (38%), Gaps = 3/123 (2%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +LLV+ S  +  + +    D  + +F   +  +A +F E+      L+I +     +   
Sbjct: 7   VLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERS--KPQLIILDLKLPDMSGE 64

Query: 64  AHVRQM-PLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQK 122
             +  +        V         +  +   + GA  FL KP N + L+ ++    +  K
Sbjct: 65  DVLDWINQNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAK 124

Query: 123 SKD 125
            +D
Sbjct: 125 LED 127


>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 = 45.6 bits (107), Expect = 4e-06
 Identities = 22/126 (17%), Positives = 42/126 (33%), Gaps = 1/126 (0%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +L+V+    +  +         F V       E       E   + +++D  +     + 
Sbjct: 5   VLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEP-FDVVILDIMLPVHDGWE 63

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQMQKS 123
                   G +  V  L    D E  + G   GA+ +L KPF+   L   +R L + +  
Sbjct: 64  ILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSE 123

Query: 124 KDENQF 129
               + 
Sbjct: 124 SKSTKL 129


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

 Score = 45.2 bits (106), Expect = 4e-06
 Identities = 24/133 (18%), Positives = 51/133 (38%), Gaps = 6/133 (4%)

Query: 1   MDS----LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESM 56
           MD+    +L+VD    + ++   +    GF         +A     +      LV+ + M
Sbjct: 1   MDTMRQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVREL--RPDLVLLDLM 58

Query: 57  EGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRE 116
              +  I   R +   + V +  L  + D   ++ G  +GA+ +++KPF  + L   +R 
Sbjct: 59  LPGMNGIDVCRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRA 118

Query: 117 LPQMQKSKDENQF 129
             +    +     
Sbjct: 119 RLRRNDDEPAEML 131


>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 = 45.1 bits (106), Expect = 5e-06
 Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 2/114 (1%)

Query: 6   LVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVID--ESMEGVLEFI 63
           +VD S   R             V EA+   EA    E+      +++D        +  +
Sbjct: 129 VVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGISLV 188

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
             +R+      + +  + +           + GAN FL +PF  E L+  +   
Sbjct: 189 RMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHN 242


>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 = 45.1 bits (106), Expect = 6e-06
 Identities = 27/124 (21%), Positives = 47/124 (37%), Gaps = 6/124 (4%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV--L 60
           L VD S ++R++   + N    M  V  A     AR+  +K   P+ L +D  M  +  L
Sbjct: 7   LSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFN-PDVLTLDVEMPRMDGL 65

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQM 120
           +F+  + ++     V +   L     E  +     GA  F+ KP                
Sbjct: 66  DFLEKLMRLR-PMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQLGIREGMLAYSEMIA 124

Query: 121 QKSK 124
           +K +
Sbjct: 125 EKVR 128


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

 Score = 44.6 bits (105), Expect = 7e-06
 Identities = 20/115 (17%), Positives = 43/115 (37%), Gaps = 2/115 (1%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
              +L+++   ++      L  + G  V +  +             P  ++ D  +    
Sbjct: 160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADGS 219

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMR 115
             I  V+ +    DV V  + +    E+++ G R      + KPF  ET++ A+ 
Sbjct: 220 SGIDAVKDILGRMDVPV--IFITAFPERLLTGERPEPTFLITKPFQPETVKAAIG 272


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

 Score = 44.6 bits (105), Expect = 8e-06
 Identities = 29/118 (24%), Positives = 48/118 (40%), Gaps = 7/118 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEGV-- 59
           ++LVD   IVR+  R L         V EA    EA      E  P+ +V+D ++ G   
Sbjct: 8   IMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYR-ETTPDIVVMDLTLPGPGG 66

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           +E   H+RQ      + +    M       +    AGA+ ++ K  +   L  A+  +
Sbjct: 67  IEATRHIRQWDGAARILI--FTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAI 122


>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 = 43.3 bits (101), Expect = 2e-05
 Identities = 23/117 (19%), Positives = 48/117 (41%), Gaps = 7/117 (5%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGF-MVFEATSVCEAREFCEKELLPNYLVIDESMEGV--L 60
           +L+ +   ++R     +  + G+ +V EA    EA E  E    P+ +++D  M     +
Sbjct: 16  VLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHK-PDLVIMDVKMPRRDGI 74

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
           +  + +          +  L      + +     AGA ++L+KPF+   L  A+   
Sbjct: 75  DAASEIASKR---IAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELA 128


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

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 10/119 (8%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           +L+V+   + R +    F+  G     A    +A E       P+ ++ D +M  +  L+
Sbjct: 10  ILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFT-PDLMICDIAMPRMNGLK 68

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFN-----RETLRFAMR 115
            + H+R    G    V  +    +   +    R G    LLKP       RE +   + 
Sbjct: 69  LLEHIRNR--GDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACLY 125


>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 = 42.2 bits (98), Expect = 4e-05
 Identities = 26/131 (19%), Positives = 50/131 (38%), Gaps = 5/131 (3%)

Query: 5   LLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFIA 64
            +VD    VR+  R+L    GF V          E    E     LV+D  M G+     
Sbjct: 8   FVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQ-HGCLVLDMRMPGMSGIEL 66

Query: 65  HVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNR----ETLRFAMRELPQM 120
             +   +   + + ++    D    +   +AGA  FL KPF      + +   ++   + 
Sbjct: 67  QEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAER 126

Query: 121 QKSKDENQFLD 131
           +++++    L+
Sbjct: 127 RQARETQDQLE 137


>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 = 41.8 bits (98), Expect = 4e-05
 Identities = 17/110 (15%), Positives = 40/110 (36%), Gaps = 7/110 (6%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV--LE 61
           + LV+       + ++  N  G  V    S     +   +    + L++ + +  +    
Sbjct: 18  VTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFS 77

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLR 111
            +  V++      V    L++     ++I  +    + +L KPF    LR
Sbjct: 78  LLDIVKEQTKQPSV----LILTTGRHELIESSEHNLS-YLQKPFAISELR 122


>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 = 40.7 bits (94), Expect = 1e-04
 Identities = 31/127 (24%), Positives = 50/127 (39%), Gaps = 7/127 (5%)

Query: 1   MDS------LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDE 54
           MD+      +L+VD    V           GF V  A    EA     +   P+ +V+D 
Sbjct: 1   MDTGVTSPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATENR-PDAIVLDI 59

Query: 55  SMEGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAM 114
           +M  +           +  DV V  L      +  +AG  AGA+ +L+KPF    L   +
Sbjct: 60  NMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARV 119

Query: 115 RELPQMQ 121
           + L + +
Sbjct: 120 KALLRRR 126


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

 Score = 40.6 bits (94), Expect = 1e-04
 Identities = 15/114 (13%), Positives = 36/114 (31%), Gaps = 11/114 (9%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFI 63
           +LL++ + ++        N  GFM     S+ +     +             +       
Sbjct: 21  VLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDLV-----MVSDKNALS 75

Query: 64  AHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMREL 117
              R     + + V         E+ +     GA+ ++ KP+       +++ L
Sbjct: 76  FVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYR------SIKAL 123


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

 Score = 38.8 bits (89), Expect = 4e-04
 Identities = 28/130 (21%), Positives = 47/130 (36%), Gaps = 3/130 (2%)

Query: 1   MDSLLLVDSSHIVRKVGRHLFNDFGFM--VFEATSVCEAREFCEKELLPNYLVIDESMEG 58
           M  + LVD   +VR+    L      +  V EA SV EA         P+  V+D  +  
Sbjct: 1   MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAA-RPDVAVLDVRLPD 59

Query: 59  VLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELP 118
                     +    D+    L      E M+    AGA+ +++K      L  A++++ 
Sbjct: 60  GNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDVG 119

Query: 119 QMQKSKDENQ 128
             +   D   
Sbjct: 120 AGRSLLDNRA 129


>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 = 38.1 bits (88), Expect = 6e-04
 Identities = 17/116 (14%), Positives = 32/116 (27%), Gaps = 5/116 (4%)

Query: 4   LLLVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEK--ELLPNYLVIDESMEG--V 59
           + ++    +  ++ +        +  E T   E      K        LVID S     V
Sbjct: 10  VRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRSIQMLVIDYSRISDDV 69

Query: 60  LEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMR 115
           L   +  + +    D     +    D E  +               + +TL   M 
Sbjct: 70  LTDYSSFKHISC-PDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMS 124


>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 = 36.4 bits (83), Expect = 0.002
 Identities = 24/129 (18%), Positives = 52/129 (40%), Gaps = 3/129 (2%)

Query: 3   SLLLVDSSHIVRKVGRHLFNDFG--FMVFEATSVCEAREFCEKELLPNYLVIDESMEGVL 60
           ++LL+D   ++R   + L +      +V EA++  +  E  E    P+ +++D +M G+ 
Sbjct: 7   TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLD-PDLILLDLNMPGMN 65

Query: 61  EFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLKPFNRETLRFAMRELPQM 120
                 +         +    +    E ++   + GA+ +LLK    E L  A+ +    
Sbjct: 66  GLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAG 125

Query: 121 QKSKDENQF 129
           +    E   
Sbjct: 126 EMVLSEALT 134


>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 = 31.1 bits (70), Expect = 0.082
 Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 40/103 (38%)

Query: 44  ELLPNYL--VIDESMEGVLEFIAHVRQ-MP--------L--GTDVFVYYLLMEVDFEKMI 90
           E +P+ +  + + + E V +++      +P        L  G    V            +
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV------------V 379

Query: 91  AG-ARA--GANSFLLK------------PFNRETLRFAMRELP 118
           +G  ++  G N  L K            PF+   L+F+ R LP
Sbjct: 380 SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP 422



 Score = 28.8 bits (64), Expect = 0.40
 Identities = 16/99 (16%), Positives = 26/99 (26%), Gaps = 30/99 (30%)

Query: 24  FGFMV-----FEATSVCEAREFCEKELLPNY---LVIDESMEGVLEFIAHVRQMPLGTDV 75
              +V     F A+ +   +E   K L P        D+      E +            
Sbjct: 18  HVLLVPTASFFIASQL---QEQFNKIL-PEPTEGFAADDEPTTPAELVGK---------- 63

Query: 76  FVYYLLMEVDFEKMIAGARAGANSFL---LKPFNRETLR 111
           F+ Y+   V+            +  L   L  F    L 
Sbjct: 64  FLGYVSSLVE-----PSKVGQFDQVLNLCLTEFENCYLE 97


>3p4t_A Putative acyl-COA dehydrogenase; ssgcid, structural genomics,
          seattle structural genomics CEN infectious disease,
          oxidoreductase; HET: FAO; 1.70A {Mycobacterium
          smegmatis} PDB: 3oib_A*
          Length = 403

 Score = 27.6 bits (61), Expect = 1.1
 Identities = 7/22 (31%), Positives = 12/22 (54%)

Query: 36 EAREFCEKELLPNYLVIDESME 57
            R F E+E+LP+    + + E
Sbjct: 36 TVRAFAEREVLPHAHEWERAGE 57


>2ix5_A Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4, flavin,
           peroxisome, glyoxysome, fatty acid metabolism, lipid
           metabolism; HET: CAA FAD; 2.7A {Arabidopsis thaliana}
           PDB: 2ix6_A*
          Length = 436

 Score = 27.3 bits (59), Expect = 1.3
 Identities = 10/59 (16%), Positives = 16/59 (27%), Gaps = 11/59 (18%)

Query: 36  EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQMPL-----------GTDVFVYYLLME 83
           + RE  EKE+ P      E  E        +  M +           G  +    +   
Sbjct: 65  KVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLSITANAIATA 123


>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A
          {Bacillus phage PHI29} PDB: 3gqk_A*
          Length = 163

 Score = 27.0 bits (60), Expect = 1.5
 Identities = 9/43 (20%), Positives = 20/43 (46%), Gaps = 3/43 (6%)

Query: 17 GRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGV 59
          G  L N+FG +++E  +  +  +F      P++   D +   +
Sbjct: 57 GAVLKNEFGGIIYEEVTTEDGVKFKRPLPNPDF---DPNKNYI 96


>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 = 26.7 bits (58), Expect = 1.7
 Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 4/23 (17%)

Query: 108  ETLRFAMRELPQMQKSKDENQFL 130
            E L+    E+P    S+D+N+FL
Sbjct: 1269 EALKLEAEEIP----SEDQNEFL 1287


>3mkh_A Nitroalkane oxidase; oxidoreductase flavoenzyme, acyl-COA
          dehydrogen flavoprotein, oxidoreductase; HET: FAD;
          2.00A {Podospora anserina}
          Length = 438

 Score = 26.2 bits (57), Expect = 2.2
 Identities = 4/19 (21%), Positives = 6/19 (31%)

Query: 36 EAREFCEKELLPNYLVIDE 54
           AR      L+P      +
Sbjct: 17 AARSLARNLLMPARQTYLQ 35


>1rx0_A Acyl-COA dehydrogenase family member 8, mitochondrial;
          flavoprotein, coenzyme A, oxidoreductase; HET: FAD 2MC;
          1.77A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1
          Length = 393

 Score = 26.0 bits (56), Expect = 2.5
 Identities = 6/19 (31%), Positives = 10/19 (52%)

Query: 36 EAREFCEKELLPNYLVIDE 54
           A +F  +E+ PN    D+
Sbjct: 29 VAFDFAAREMAPNMAEWDQ 47


>1egd_A Medium chain acyl-COA dehydrogenase; flavoprotein, electron
          transfer; HET: FAD; 2.40A {Homo sapiens} SCOP: a.29.3.1
          e.6.1.1 PDB: 1egc_A* 1ege_A* 1t9g_A* 2a1t_A* 1udy_A*
          3mdd_A* 3mde_A*
          Length = 396

 Score = 25.9 bits (56), Expect = 2.8
 Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 12/60 (20%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQMPL------------GTDVFVYYLLME 83
           AR+F  +E++P     D++ E  +  I    ++ L            G   F   L+ E
Sbjct: 26 TARKFAREEIIPVAAEYDKTGEYPVPLIRRAWELGLMNTHIPENCGGLGLGTFDACLISE 85


>2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid
          metabolism, FAD, polymorphism, flavoprotein,
          mitochondrion, disease mutation; HET: FAD COS; 1.9A
          {Homo sapiens} PDB: 1jqi_A*
          Length = 391

 Score = 25.9 bits (56), Expect = 2.8
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 36 EAREFCEKELLPNYLVIDE 54
            R+F EKEL P    +D+
Sbjct: 16 TCRDFAEKELFPIAAQVDK 34


>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural
          genomics center for infectious disease, ssgcid; HET:
          FDA; 2.10A {Mycobacterium thermoresistibile}
          Length = 393

 Score = 25.9 bits (57), Expect = 2.8
 Identities = 9/34 (26%), Positives = 13/34 (38%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
            R   EKE+ P    +DE      E +A +   
Sbjct: 29 AIRALAEKEIAPYAAEVDEKARFPEEALAALNSS 62


>2pg0_A Acyl-COA dehydrogenase; GK1316, structural genomics, PSI, protein
          structure initiative; HET: FAD; 1.80A {Geobacillus
          kaustophilus HTA426}
          Length = 385

 Score = 25.9 bits (56), Expect = 3.1
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
            R+F EKE  P+Y   ++       F A + + 
Sbjct: 20 AFRKFLEKEAYPHYNDWEKRGIIPRSFWAKMGEN 53


>3nf4_A Acyl-COA dehydrogenase; seattle structural genomics center for
          infectious disease, S FAD, FADH, tuberculosis,
          oxidoredu; HET: FAD; 2.35A {Mycobacterium
          thermoresistibile}
          Length = 387

 Score = 25.7 bits (56), Expect = 3.2
 Identities = 5/19 (26%), Positives = 8/19 (42%)

Query: 36 EAREFCEKELLPNYLVIDE 54
            RE  +K L P     ++
Sbjct: 26 LTREIADKVLDPIVDRHEK 44


>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring
           E3, PIAS, ubiquitin, UBC9, cytoplasm, metal-binding,
           nucleus; 2.60A {Saccharomyces cerevisiae}
          Length = 371

 Score = 25.4 bits (55), Expect = 4.0
 Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 8/41 (19%)

Query: 29  FEATSVCEARE--------FCEKELLPNYLVIDESMEGVLE 61
           F+A     ++          C+ ++    L I E ++ +L+
Sbjct: 274 FDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDILQ 314


>3mpi_A Glutaryl-COA dehydrogenase; alpha-beta fold, oxidoreductase; HET:
          FAD GRA; 2.05A {Desulfococcus multivorans} PDB: 3mpj_A*
          Length = 397

 Score = 25.6 bits (56), Expect = 4.1
 Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 2/34 (5%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
          E R F  K+++P     D   E    +   VR M
Sbjct: 15 EVRNFVNKKIVPFADQWDN--ENHFPYEEAVRPM 46


>3owa_A Acyl-COA dehydrogenase; structural genomics, center for
          structural genomics of infec diseases, csgid,
          alpha-structure, beta-barrel; HET: MSE FAD 1PE; 1.97A
          {Bacillus anthracis}
          Length = 597

 Score = 25.4 bits (55), Expect = 4.3
 Identities = 4/20 (20%), Positives = 9/20 (45%)

Query: 36 EAREFCEKELLPNYLVIDES 55
             +F   E+LP    +++ 
Sbjct: 43 TTEDFIVNEVLPELEYLEQH 62


>1ukw_A Acyl-COA dehydrogenase; oxidoreductase, riken structural
          genomics/proteomics initiative, RSGI, structural
          genomics; HET: FAD; 2.40A {Thermus thermophilus} SCOP:
          a.29.3.1 e.6.1.1
          Length = 379

 Score = 25.5 bits (55), Expect = 4.3
 Identities = 9/34 (26%), Positives = 15/34 (44%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
           AR F ++ +LP     DE  E     I  + ++
Sbjct: 15 LARRFAKEVILPVAQEYDEKEEVPWPVIEKLHEV 48


>2jif_A Short/branched chain specific acyl-COA dehydrogenase;
          mitochondrion, oxidoreductase, transit peptide, fatty
          acid metabolism, FAD, acetylation; HET: FAD COS; 2.0A
          {Homo sapiens}
          Length = 404

 Score = 25.5 bits (55), Expect = 4.4
 Identities = 4/19 (21%), Positives = 11/19 (57%)

Query: 36 EAREFCEKELLPNYLVIDE 54
            ++F ++++ P    +DE
Sbjct: 39 SVKKFAQEQIAPLVSTMDE 57


>2dvl_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national
          project on protein structural and functional analyses;
          HET: FAD; 2.50A {Thermus thermophilus HB8}
          Length = 372

 Score = 25.1 bits (54), Expect = 4.9
 Identities = 5/34 (14%), Positives = 10/34 (29%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
            R    + L P     D   E     +  + ++
Sbjct: 13 AVRRVAREVLYPLAPEYDRKAEYPWPQLKALAEL 46


>2d29_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national
          project on protein structural and functional analyses;
          HET: FAD; 1.65A {Thermus thermophilus HB8} SCOP:
          a.29.3.1 e.6.1.1 PDB: 1ws9_A 2cx9_A*
          Length = 387

 Score = 25.1 bits (54), Expect = 4.9
 Identities = 6/34 (17%), Positives = 13/34 (38%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
            REF + E+ P     D +     + +  + + 
Sbjct: 17 PFREFLKAEVAPGAAERDRTGAFPWDLVRKLAEF 50


>1siq_A GCD, glutaryl-COA dehydrogenase; acyl-COA dehydrogenase,
          decarboxylation, flavin protein, oxidoreductase; HET:
          FAD; 2.10A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 PDB:
          2r0n_A* 1sir_A* 2r0m_A*
          Length = 392

 Score = 25.3 bits (54), Expect = 5.0
 Identities = 5/19 (26%), Positives = 11/19 (57%)

Query: 36 EAREFCEKELLPNYLVIDE 54
            R +C++ L+P  L+ + 
Sbjct: 24 TFRTYCQERLMPRILLANR 42


>1buc_A Butyryl-COA dehydrogenase; acyl-COA dehydrogenase (flavoprotein);
          HET: CAA FAD; 2.50A {Megasphaera elsdenii} SCOP:
          a.29.3.1 e.6.1.1
          Length = 383

 Score = 25.2 bits (54), Expect = 5.1
 Identities = 9/34 (26%), Positives = 13/34 (38%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
           A +F EK+L P     D       E I  +  +
Sbjct: 15 LAHDFGEKKLAPTVTERDHKGIYDKELIDELLSL 48


>2eba_A Putative glutaryl-COA dehydrogenase; thermus thermophilius, FAD,
          structural genomics, NPPSFA; HET: FAD; 2.21A {Thermus
          thermophilus HB8}
          Length = 385

 Score = 24.8 bits (53), Expect = 5.9
 Identities = 10/34 (29%), Positives = 13/34 (38%)

Query: 36 EAREFCEKELLPNYLVIDESMEGVLEFIAHVRQM 69
           AR F EKE LP+     E        I    ++
Sbjct: 21 AARRFLEKEALPHIRDWWEEGVFPTHLIPRFAEL 54


>1ea0_A Glutamate synthase [NADPH] large chain; oxidoreductase, iron sulphur
            flavoprotein; HET: OMT FMN AKG; 3.0A {Azospirillum
            brasilense} SCOP: b.80.4.1 c.1.4.1 d.153.1.1 PDB: 2vdc_A*
          Length = 1479

 Score = 25.0 bits (55), Expect = 6.0
 Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 55   SMEGVLEFIAHVRQMPLGTDVFVYYLLMEVDFEKMIAG-ARAGAN 98
            S+E + + I  ++Q+     V V  L+       + AG A+A A+
Sbjct: 976  SIEDLAQLIYDLKQINPDAKVTV-KLVSRSGIGTIAAGVAKANAD 1019


>2wf7_A Beta-PGM, beta-phosphoglucomutase; transition state analogue,
          haloacid dehalogenase superfamily, isomerase,
          phosphotransferase; HET: G7P; 1.05A {Lactococcus
          lactis} PDB: 1o03_A* 1z4n_A* 1z4o_A* 1zol_A 2wf5_A*
          2wf6_A* 1o08_A* 2wf8_A* 2wf9_A* 2wfa_A 2whe_A 1lvh_A*
          3fm9_A
          Length = 221

 Score = 24.7 bits (53), Expect = 6.6
 Identities = 7/64 (10%), Positives = 22/64 (34%)

Query: 6  LVDSSHIVRKVGRHLFNDFGFMVFEATSVCEAREFCEKELLPNYLVIDESMEGVLEFIAH 65
          + D++    +  + L  + G    +     + +    ++ L   L + +      EF   
Sbjct: 13 ITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKEL 72

Query: 66 VRQM 69
           ++ 
Sbjct: 73 AKRK 76


>3l5k_A Protein GS1, haloacid dehalogenase-like hydrolase domain-
           containing protein 1A; HDHD1A, haloacid
           dehalogenase-like hydrolase domain containing 1A; 2.00A
           {Homo sapiens}
          Length = 250

 Score = 24.7 bits (53), Expect = 6.7
 Identities = 12/86 (13%), Positives = 23/86 (26%), Gaps = 23/86 (26%)

Query: 6   LVDSSHIVRKVGRHLFNDFG-----------------------FMVFEATSVCEAREFCE 42
           L+D+  +   V + + N +                          V +     E      
Sbjct: 41  LLDTERLYSVVFQEICNRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQLPMSKEELVEES 100

Query: 43  KELLPNYLVIDESMEGVLEFIAHVRQ 68
           +  L         M G  + I H+R+
Sbjct: 101 QTKLKEVFPTAALMPGAEKLIIHLRK 126


>3kuq_A RHO GTPase-activating protein 7; structural genomics consortium,
           GTPase activation, SGC, alternative splicing, cytoplasm,
           phosphoprotein; 2.30A {Homo sapiens}
          Length = 228

 Score = 24.6 bits (53), Expect = 7.1
 Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 3/70 (4%)

Query: 62  FIAHVRQMPLGTDVFVYYLLMEVDFEKMIAGARAGANSFLLK---PFNRETLRFAMRELP 118
              + R +P               ++ +    R  A    +      NRE L+  +  L 
Sbjct: 95  LKQYFRDLPEPLMTNKLSETFLQIYQYVPKDQRLQAIKAAIMLLPDENREVLQTLLYFLS 154

Query: 119 QMQKSKDENQ 128
            +  +  ENQ
Sbjct: 155 DVTAAVKENQ 164


>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA,
          national project on protein structural and functional
          analyses; HET: FAD; 2.30A {Thermus thermophilus}
          Length = 577

 Score = 24.5 bits (52), Expect = 9.1
 Identities = 6/20 (30%), Positives = 10/20 (50%)

Query: 36 EAREFCEKELLPNYLVIDES 55
            R F E+E+LP    ++  
Sbjct: 38 TTRTFVEREVLPLLERMEHG 57


>1ivh_A Isovaleryl-COA dehydrogenase; oxidoreductase, acyl-COA
          dehydrogenase, flavoprotein, isovaleric acidemia; HET:
          FAD COS; 2.60A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1
          Length = 394

 Score = 24.4 bits (52), Expect = 9.7
 Identities = 7/22 (31%), Positives = 10/22 (45%)

Query: 36 EAREFCEKELLPNYLVIDESME 57
             +F ++ L P    ID S E
Sbjct: 23 TMAKFLQEHLAPKAQEIDRSNE 44


  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
   0.327    0.141    0.404 

Gapped
Lambda     K      H
   0.267   0.0642    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,115,687
Number of extensions: 48634
Number of successful extensions: 323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 134
Length of query: 133
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 51
Effective length of database: 3,705,222
Effective search space: 188966322
Effective search space used: 188966322
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.6 bits)