RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780526|ref|YP_003064939.1| putative transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62] (223 letters) >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 = 103 bits (257), Expect = 4e-23 Identities = 56/224 (25%), Positives = 103/224 (45%), Gaps = 9/224 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + D L +G L R + L+ G ++ Sbjct: 9 IVEDEESLADPLAFLLRKEGFEATVVTD--GPAALAEFDRAGADIVLLDLMLPGMSGTDV 66 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL---- 119 + +RA S VP+I ++ S + + G DD V KP RE++AR+ A+ RR Sbjct: 67 CKQLRARSSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRGGDDD 126 Query: 120 -KVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIY 178 ++S+ E+GP+R+ + V G+ LP +E +LEYLM N G+ + + Q+ ++ Sbjct: 127 SEMSDGVLESGPVRMDVERHVVSVNGDTITLPLKEFDLLEYLMRNSGRVLTRGQLIDRVW 186 Query: 179 GLFDEAVEENVVESHISKLRKKLR-NKLGFDPVDSKRFLGYSID 221 G D + ++ H+ +LR K+ + + + R LGY ++ Sbjct: 187 G-ADYVGDTKTLDVHVKRLRSKIEADPANPVHLVTVRGLGYKLE 229 >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 = 79.9 bits (196), Expect = 4e-16 Identities = 46/217 (21%), Positives = 98/217 (45%), Gaps = 5/217 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEA-FLIGKGEKVLE 62 +++D + D + +++ EE + + E + ++ + Sbjct: 7 VVEDERDLADLITEALKKEMFTVDVCYD--GEEGMYMALNEPFDVVILDIMLPVHDGWEI 64 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 L + + P++ ++ ++ + + G DD + KP RE++ARV A+ RR S Sbjct: 65 LKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRKSES 124 Query: 123 -NNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLF 181 + + G + + + + + L ++E +ILEYL+ N+ + V K ++ ++ F Sbjct: 125 KSTKLVCGDLILDTATKKAYRGSKEIDLTKKEYQILEYLVMNKNRVVTKEELQEHLWS-F 183 Query: 182 DEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGY 218 D+ V +V+ SHI LRKK+ + + R +GY Sbjct: 184 DDEVFSDVLRSHIKNLRKKVDKGFKKKIIHTVRGIGY 220 >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 = 77.1 bits (189), Expect = 3e-15 Identities = 44/217 (20%), Positives = 90/217 (41%), Gaps = 12/217 (5%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GEKVLE 62 ++DD + G E++L V ++ L G ++ Sbjct: 7 VVDDDKNILKKVSEKLQQLGRVKTFLTG---EDFLNDEEAFHVVVLDVMLPDYSGYEICR 63 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 + + + +I ++ ++ L F++G DD V KP + +LARV R K Sbjct: 64 MIK--ETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK-- 119 Query: 123 NNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFD 182 + G +++ + G ++G+ LP++E IL +L N GK V + ++ + Sbjct: 120 KGLYDFGDLKIDATGFTVFLKGKRIHLPKKEFEILLFLAENAGKVVTREKLLETFWE--- 176 Query: 183 EAVEENVVESHISKLRKKLRNKLGF-DPVDSKRFLGY 218 + V VV++ I ++RK + + + + +GY Sbjct: 177 DPVSPRVVDTVIKRIRKAIEDDPNRPRYIKTIWGVGY 213 >2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} Length = 238 Score = 75.6 bits (185), Expect = 9e-15 Identities = 42/217 (19%), Positives = 85/217 (39%), Gaps = 5/217 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD A + + + +G + L + + L+ G +++ Sbjct: 10 VVDDDASLAEMLTIVLRGEGFDTAVIGD--GTQALTAVRELRPDLVLLDLMLPGMNGIDV 67 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL-KVS 122 R++RA S VP++ ++ + +SG DD + KP +E++ARV A RR Sbjct: 68 CRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRRNDDEP 127 Query: 123 NNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFD 182 + + GE L E +L L + + + ++G + Sbjct: 128 AEMLSIADVEIDVPAHKVTRNGEQISLTPLEFDLLVALARKPRQVFTRDVLLEQVWG-YR 186 Query: 183 EAVEENVVESHISKLRKKL-RNKLGFDPVDSKRFLGY 218 + +V H+ +LR K+ ++ V + R +GY Sbjct: 187 HPADTRLVNVHVQRLRAKVEKDPENPTVVLTVRGVGY 223 >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 = 68.4 bits (166), Expect = 1e-12 Identities = 54/222 (24%), Positives = 97/222 (43%), Gaps = 8/222 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + V G + E L+S+ AI + + + Sbjct: 12 VVDDDSDVLASLERGLRLSGFEVATAVD--GAEALRSATENRPDAIVLDINMPVLDGVSV 69 Query: 64 PRIIRAH-SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 +RA + VP+ +S S+ + ++G DD + KP E++ARV A+ RR + Sbjct: 70 VTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRRGST 129 Query: 123 NNRA----ETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIY 178 + GP+ V GR V G L +RE +L L ++ +++ Q+ ++ Sbjct: 130 ATSSSETITVGPLEVDIPGRRARVNGVDVDLTKREFDLLAVLAEHKTAVLSRAQLLELVW 189 Query: 179 GLFDEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGYSI 220 G +D A + NVV+ I LR+KL G + + R +G+ + Sbjct: 190 G-YDFAADTNVVDVFIGYLRRKLEAGGGPRLLHTVRGVGFVL 230 >2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, transcription; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis H37RV} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A* Length = 388 Score = 59.6 bits (143), Expect = 5e-10 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%) Query: 129 GPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEEN 188 GP+++ DG V ++R +L L+ NR + V + +A++ + + Sbjct: 17 GPLQMTIDGT------PVPSGTPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARA 70 Query: 189 VVESHISKLRKKLR 202 + S++S LRK L Sbjct: 71 SIHSYVSNLRKLLG 84 >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 = 59.9 bits (144), Expect = 5e-10 Identities = 35/202 (17%), Positives = 76/202 (37%), Gaps = 16/202 (7%) Query: 3 VLIDDRALVKDG---YIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 +LIDD +++ G I++ D V E N + E +S + + G + Sbjct: 9 LLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLE 68 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 L+ R ++ + +S++ + + G D + K + ++L + Sbjct: 69 TLDKLREKSLSGRIVVFSVSNHE--EDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGE 126 Query: 120 KVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYG 179 V + A T + + +V L RER IL+ + ++ ++ Sbjct: 127 MVLSE-ALTPVLAASLRANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLD----- 180 Query: 180 LFDEAVEENVVESHISKLRKKL 201 + E+ V+ H+ + KK+ Sbjct: 181 -----ITESTVKVHVKHMLKKM 197 >2jzy_A Transcriptional regulatory protein PCOR; two-component-system response regulator, effector domain, DNA-binding, phosphoprotein, plasmid; NMR {Klebsiella pneumoniae} Length = 112 Score = 59.5 bits (144), Expect = 6e-10 Identities = 19/93 (20%), Positives = 42/93 (45%), Gaps = 1/93 (1%) Query: 129 GPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEEN 188 + V R G+ L +E +LE L+ G+ + ++ I S ++ + + N Sbjct: 9 ADMTVDMVRRTVIRSGKKIHLTGKEYVLLELLLQRTGEVLPRSLISSLVWN-MNFDSDTN 67 Query: 189 VVESHISKLRKKLRNKLGFDPVDSKRFLGYSID 221 V++ + +LR K+ + + + R GY ++ Sbjct: 68 VIDVAVRRLRSKIDDDFEPKLIHTVRGAGYVLE 100 >2k4j_A Putative transcriptional regulator; response regulator, acid resistance, DNA-binding, phosphoprotein, transcription regulation; NMR {Helicobacter pylori J99} Length = 115 Score = 56.1 bits (135), Expect = 7e-09 Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 2/97 (2%) Query: 126 AETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAV 185 + RV D R+ + + L R E IL L++ +G ++ I + Sbjct: 19 GDANIFRVDKDSREVYMHEKKLDLTRAEYEILSLLISKKGYVFSRESIAIESES-INPES 77 Query: 186 EENVVESHISKLRKKL-RNKLGFDPVDSKRFLGYSID 221 ++ I +LR K+ +N + S R +GY ++ Sbjct: 78 SNKSIDVIIGRLRSKIEKNPKQPQYIISVRGIGYKLE 114 >2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, symmetric dimer, signaling protein; NMR {Helicobacter pylori J99} Length = 223 Score = 55.8 bits (133), Expect = 7e-09 Identities = 28/87 (32%), Positives = 48/87 (55%), Gaps = 8/87 (9%) Query: 132 RVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVE 191 ++ GR+ EV+G+ F +L +L +R + V+K Q+ AI+ E V NV+E Sbjct: 134 KIIYKGREVEVKGKPF-------EVLTHLARHRDQIVSKEQLLDAIWE-EPEMVTPNVIE 185 Query: 192 SHISKLRKKLRNKLGFDPVDSKRFLGY 218 I+++R+K+ LG V++ R GY Sbjct: 186 VAINQIRQKMDKPLGISTVETVRRRGY 212 >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 = 55.1 bits (132), Expect = 1e-08 Identities = 28/202 (13%), Positives = 65/202 (32%), Gaps = 13/202 (6%) Query: 3 VLIDDRALVKDG---YIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 ++ D + + + + F+ L EE S + I+ I Sbjct: 11 RMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKPESRSIQMLVIDYSRISDDVL 70 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + + I+ ++ L F + + V ++ ++ I + Sbjct: 71 TDYSSFKHISCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKILQDE 130 Query: 120 KVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYG 179 + I + G L +RE++I++ L + +I ++ Sbjct: 131 MWLTRKLAQEYILHYRAGNSVVTSQMYAKLTKREQQIIKLLGSGASNI----EIADKLF- 185 Query: 180 LFDEAVEENVVESHISKLRKKL 201 V EN V++H+ + KK+ Sbjct: 186 -----VSENTVKTHLHNVFKKI 202 >1gxq_A PHOB, phosphate regulon transcriptional regulatory protein; transcriptional activator, helix-winged-helix, sensory transduction; 2.0A {Escherichia coli} SCOP: a.4.6.1 PDB: 1gxp_A 1qqi_A 2z33_A Length = 106 Score = 53.4 bits (128), Expect = 4e-08 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 1/92 (1%) Query: 127 ETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVE 186 E + + E + E ++L + M + + ++ Q+ + ++G + VE Sbjct: 10 EMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWG-TNVYVE 68 Query: 187 ENVVESHISKLRKKLRNKLGFDPVDSKRFLGY 218 + V+ HI +LRK L V + R GY Sbjct: 69 DRTVDVHIRRLRKALEPGGHDRMVQTVRGTGY 100 >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 = 53.4 bits (128), Expect = 4e-08 Identities = 32/115 (27%), Positives = 50/115 (43%), Gaps = 2/115 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + D +G + + E L+ E I L+ LE+ Sbjct: 6 IVDDEKPISDIIKFNMTKEGYEVVTAFN--GREALEQFEAEQPDIIILDLMLPEIDGLEV 63 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + IR S VP++ +S S + + G DD V KP +RE+ ARV A+ RR Sbjct: 64 AKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR 118 >1opc_A OMPR, OMPRC; transcription regulation, response regulator, winged helix, osmoregulation; 1.95A {Escherichia coli} SCOP: a.4.6.1 PDB: 1odd_A 2jpb_A Length = 110 Score = 52.6 bits (126), Expect = 7e-08 Identities = 17/91 (18%), Positives = 43/91 (47%), Gaps = 2/91 (2%) Query: 129 GPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEEN 188 G ++ R+ + E PL E +L+ L+++ + +++ ++ + G + + E Sbjct: 12 GKFKLNLGTREMFREDEPMPLTSGEFAVLKALVSHPREPLSRDKLMNLARG-REYSAMER 70 Query: 189 VVESHISKLRKKL-RNKLGFDPVDSKRFLGY 218 ++ IS+LR+ + + + + LGY Sbjct: 71 SIDVQISRLRRMVEEDPAHPRYIQTVWGLGY 101 >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 = 1e-07 Identities = 15/124 (12%), Positives = 41/124 (33%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + G ++E + E S + +G+G ++ Sbjct: 10 IVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQT 69 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVSN 123 I+ S++P++ ++ + V K + ++ V R + + Sbjct: 70 ALAIQQISELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEANV 129 Query: 124 NRAE 127 + E Sbjct: 130 HANE 133 >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 = 51.6 bits (123), Expect = 1e-07 Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 + L R++R Q+ +IGIS + + G +D +N+P E+ RV+ Sbjct: 185 ISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLE 244 Query: 118 RLKVSNN 124 L+ N+ Sbjct: 245 ALEQFNS 251 >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 = 51.3 bits (122), Expect = 2e-07 Identities = 17/115 (14%), Positives = 45/115 (39%), Gaps = 1/115 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + D + +G +E + + +++ L L Sbjct: 8 IVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIENEFFNLALFXIKLPDMEGTELLE 67 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + + + I ++ Y SL+ ++ ++G D + KP++ R++L ++ Sbjct: 68 -KAHKLRPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDE 121 >2zwm_A Transcriptional regulatory protein YYCF; two-component system, response regulator, dimerization domain, phosphorylation site, cytoplasm; 2.04A {Bacillus subtilis} Length = 130 Score = 49.5 bits (118), Expect = 6e-07 Identities = 21/58 (36%), Positives = 31/58 (53%) Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 +E+ R +R +P+I ++ S + + G DD V KP RE+LARV A RR Sbjct: 62 VEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRR 119 >3cg0_A Response regulator receiver modulated diguanylate cyclase with PAS/PAC sensor; signal receiver domain; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140 Score = 49.3 bits (117), Expect = 7e-07 Identities = 15/118 (12%), Positives = 36/118 (30%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D L G + G E + A+ ++ +E Sbjct: 14 IVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVET 73 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKV 121 + A +P+I I+ ++T + KP+ + + + K+ Sbjct: 74 AARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKL 131 >3c3w_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 2.20A {Mycobacterium tuberculosis} Length = 225 Score = 49.2 bits (116), Expect = 7e-07 Identities = 38/202 (18%), Positives = 71/202 (35%), Gaps = 17/202 (8%) Query: 3 VLIDDRALVKDGYIALFGDDG---VSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 L+DD +V+ G + L G D V E + E + ++ + G G + Sbjct: 5 FLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIE 64 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + ++ + + ++ Y S + LD +G V K I E+ A Sbjct: 65 LCR--DLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMEL--ARAVKDVGA 120 Query: 120 KVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYG 179 S + E Q + L +ER +L L + ++F Sbjct: 121 GRSLLDNRAAAALMAKLRGAAEKQDPLSGLTDQERTLLGLLSEGLTNKQIADRMF----- 175 Query: 180 LFDEAVEENVVESHISKLRKKL 201 + E V++++S+L KL Sbjct: 176 -----LAEKTVKNYVSRLLAKL 192 >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 = 49.1 bits (116), Expect = 7e-07 Identities = 19/176 (10%), Positives = 60/176 (34%), Gaps = 12/176 (6%) Query: 4 LIDDRALVKDGYIALFGDDG--VSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVL 61 + +D AL++ + ++G + E + E E + + D+ ++ + + + Sbjct: 18 IAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAEL-HKPDLVIMDVKMPRR--DGI 74 Query: 62 ELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKV 121 + I + P++ ++ + D+G + KP +++ + R + Sbjct: 75 DAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFRE 134 Query: 122 SN-------NRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAK 170 +E R + +Q + + ++ +R + + Sbjct: 135 ITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKR 190 >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 = 48.4 bits (115), Expect = 1e-06 Identities = 18/118 (15%), Positives = 41/118 (34%), Gaps = 4/118 (3%) Query: 4 LIDDRALVKDGYIALFGDDG--VSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVL 61 ++DD +F +G + + E ++ ++ + + + Sbjct: 41 IVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNH-YPNIDIVTLXITMPKMDGI 99 Query: 62 E-LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 L I+ +I IS Q D G + KP+ ++L RV +++ + Sbjct: 100 TCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSVFVK 157 >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 = 48.6 bits (115), Expect = 1e-06 Identities = 27/119 (22%), Positives = 57/119 (47%), Gaps = 2/119 (1%) Query: 1 MFVLI-DDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 M VL+ +D AL++ D G ++ + ++ + D++ ++ L + + Sbjct: 1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDE-DG 59 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + + R +P++ ++ S Q ++ +G DD V KP H E++AR+ A+ RR Sbjct: 60 LSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118 >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 = 1e-06 Identities = 19/119 (15%), Positives = 52/119 (43%), Gaps = 5/119 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D A +++ + +G +++ + I + G ++ Sbjct: 7 VVEDEAPIREMVCFVLEQNGFQPVEAE--DYDSAVNQLNEPWPDLILLAWMLPGGSGIQF 64 Query: 64 PRIIRAHSQ---VPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + +R S +P++ ++ + + ++G DD + KP +E++AR+ A+ RR+ Sbjct: 65 IKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMRRI 123 >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 = 48.2 bits (114), Expect = 2e-06 Identities = 15/118 (12%), Positives = 40/118 (33%), Gaps = 1/118 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GEKVLE 62 ++DD A V+ + D G + +S L V ++ + G G + Sbjct: 12 IVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIR 71 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 + ++ ++ + + V D + KP + +++ + ++ Sbjct: 72 AILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGFVR 129 >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 = 48.0 bits (114), Expect = 2e-06 Identities = 27/117 (23%), Positives = 52/117 (44%), Gaps = 3/117 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD A+ ++ I G+ G + E E L ++ + + L + E L+L Sbjct: 12 VVDDNAVNREALILYLKSRGIDAVGADGAE-EARLYLHYQKRIGLMITDLRMQPESGLDL 70 Query: 64 PRIIRA--HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 R IRA + + +I +S ++ +D GV D + KP+ ++L V + Sbjct: 71 IRTIRASERAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKELKI 127 >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 = 47.6 bits (114), Expect = 2e-06 Identities = 21/58 (36%), Positives = 31/58 (53%) Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 +E+ R +R +P+I ++ S + + G DD V KP RE+LARV A RR Sbjct: 62 VEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLRR 119 >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 = 47.6 bits (112), Expect = 2e-06 Identities = 29/199 (14%), Positives = 69/199 (34%), Gaps = 23/199 (11%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNS-LEFEEWLQSSAREDVSAIEAFLIGKGEKVLE 62 ++DD V++G L G +E F+ F E + + G ++ E Sbjct: 9 VVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQE 68 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 +P++ I+ + + T+ +G + + KP + +L + + Sbjct: 69 QLT--AISDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQL---- 122 Query: 123 NNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFD 182 R + +++ L RE+++L+ + + ++ Sbjct: 123 ------NAERRQARETQDQLEQLFSSLTGREQQVLQLTIRGLMNKQIAGELG-------- 168 Query: 183 EAVEENVVESHISKLRKKL 201 + E V+ H + +KL Sbjct: 169 --IAEVTVKVHRHNIMQKL 185 >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 = 47.4 bits (112), Expect = 2e-06 Identities = 26/115 (22%), Positives = 46/115 (40%), Gaps = 2/115 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D ++ DG+ + + + L +A I L +E Sbjct: 6 IVEDEQAIRRFLRTALEGDGMRVFEAET--LQRGLLEAATRKPDLIILDLGLPDGDGIEF 63 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 R +R S VP+I +S + D+G DD ++KP E+ AR+ RR Sbjct: 64 IRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRR 118 >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 = 46.7 bits (111), Expect = 4e-06 Identities = 12/65 (18%), Positives = 29/65 (44%) Query: 57 GEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116 G ++L+ R A S +P++ ++ + + +G V KP + ++ I+ Sbjct: 64 GLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIF 123 Query: 117 RRLKV 121 +L + Sbjct: 124 EKLGM 128 >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 = 46.5 bits (110), Expect = 5e-06 Identities = 12/124 (9%), Positives = 41/124 (33%), Gaps = 5/124 (4%) Query: 4 LIDD----RALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 +I+D ++ ++ +N + + L + + V + G Sbjct: 13 IIEDDKEFADMLTQ-FLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFS 71 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + + A + + +I ++ + G + KP++ + + + + Sbjct: 72 ICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQK 131 Query: 120 KVSN 123 K ++ Sbjct: 132 KATS 135 >3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137 Score = 46.6 bits (110), Expect = 5e-06 Identities = 20/121 (16%), Positives = 46/121 (38%), Gaps = 3/121 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GEKVLE 62 L++D + Y D+ + + ++ + ++ L GE VL+ Sbjct: 9 LVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLD 68 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 + +I + + S+ ++ G +D + KPI+ + VA +R K+ Sbjct: 69 WIN--QNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAKLE 126 Query: 123 N 123 + Sbjct: 127 D 127 >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 = 46.4 bits (110), Expect = 5e-06 Identities = 13/64 (20%), Positives = 26/64 (40%) Query: 57 GEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116 G +L+ R A + I ++ G ++V+ KP ++ A + A++ Sbjct: 66 GLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVF 125 Query: 117 RRLK 120 LK Sbjct: 126 GALK 129 >3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140 Score = 46.2 bits (110), Expect = 6e-06 Identities = 11/64 (17%), Positives = 23/64 (35%) Query: 57 GEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116 G +VL R + P+I + + V D + KP + + V ++ Sbjct: 66 GLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVL 125 Query: 117 RRLK 120 + + Sbjct: 126 KICQ 129 >3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} Length = 286 Score = 46.1 bits (109), Expect = 6e-06 Identities = 19/126 (15%), Positives = 42/126 (33%), Gaps = 2/126 (1%) Query: 1 MFVLIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKV 60 ++I+D ++ AL + G + + E + R + + G Sbjct: 162 EVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVTRRTPGLVLADIQLADGSSG 221 Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 ++ + I VP+I I+ +P + L ++ KP + A + Sbjct: 222 IDAVKDILGRMDVPVIFITAFP--ERLLTGERPEPTFLITKPFQPETVKAAIGQALFFHP 279 Query: 121 VSNNRA 126 +A Sbjct: 280 RRTAKA 285 >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 = 46.0 bits (109), Expect = 6e-06 Identities = 17/128 (13%), Positives = 40/128 (31%), Gaps = 4/128 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + + + + L + I + E+ Sbjct: 10 VVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEV 69 Query: 64 PRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHH-REILARVAAIYRRL 119 +R P++ ++D S +G VV+K ++ + R+ AI+ Sbjct: 70 MSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSYW 129 Query: 120 KVSNNRAE 127 N+ E Sbjct: 130 LTVNHCQE 137 >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 = 45.8 bits (108), Expect = 7e-06 Identities = 18/118 (15%), Positives = 42/118 (35%), Gaps = 1/118 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGF-NSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLE 62 L+D + I+ +G + N++E + + G + Sbjct: 13 LVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFN 72 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 + + +P+I +S + + D G D + KP++ + AR+ + + L Sbjct: 73 SLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRVLKLLY 130 >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 = 45.5 bits (107), Expect = 1e-05 Identities = 25/116 (21%), Positives = 48/116 (41%), Gaps = 2/116 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + + + F +G ++ S + + V I + E L L Sbjct: 7 IVEDEPVTQARLQSYFTQEGYTVSVTAS--GAGLREIMQNQSVDLILLDINLPDENGLML 64 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 R +R S V +I ++ + + G DD V KP+ RE++ RV + R+ Sbjct: 65 TRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRI 120 >3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136 Score = 45.5 bits (107), Expect = 1e-05 Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 1/118 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+D + + L V+++ F S E Q S IEA L K + +EL Sbjct: 11 LVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSGIEL 70 Query: 64 PRIIR-AHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 + +P I ++ + T + + D + KP ++ V I K Sbjct: 71 LETLVKRGFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGAK 128 >2z9m_A Response regulator YYCF; two-component system, YYCG, helix-turn- helix motif, DNA-binding domain, phosphorylation, transcription; 1.87A {Staphylococcus aureus} PDB: 2zxj_A 2d1v_A Length = 120 Score = 45.5 bits (107), Expect = 1e-05 Identities = 21/103 (20%), Positives = 47/103 (45%), Gaps = 2/103 (1%) Query: 122 SNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLF 181 N I ++ D + +GE L RE + YL + G+ + + + ++G + Sbjct: 10 VTNEITIKDIVIYPDAYSIKKRGEDIELTHREFELFHYLSKHMGQVMTREHLLQTVWG-Y 68 Query: 182 DEAVEENVVESHISKLRKKLRNKLG-FDPVDSKRFLGYSIDWN 223 D + V+ I +LR+K+ + + + ++R +GY + + Sbjct: 69 DYFGDVRTVDVTIRRLREKIEDDPSHPEYIVTRRGVGYFLQQH 111 >2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics, protein structure initiative; 2.89A {Clostridium difficile 630} Length = 136 Score = 45.2 bits (106), Expect = 1e-05 Identities = 26/117 (22%), Positives = 48/117 (41%), Gaps = 2/117 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +ID + G+S++ EE + I +I L Sbjct: 9 IIDGDKDNCQKLKGFLEEKGISIDLAY--NCEEAIGKIFSNKYDLIFLEIILSDGDGWTL 66 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 + IR + P++ ++ Q+ L+ +SG DD + KP++ + A+V AI RR+ Sbjct: 67 CKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMN 123 >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 = 45.0 bits (106), Expect = 1e-05 Identities = 17/113 (15%), Positives = 40/113 (35%), Gaps = 1/113 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GEKVLE 62 L+DD A+++ +G + + + S D+ + + G VL+ Sbjct: 7 LVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTVLK 66 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAI 115 + ++P+I ++ + G V+ KP + + V + Sbjct: 67 KLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHL 119 >3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154 Score = 45.2 bits (106), Expect = 1e-05 Identities = 18/131 (13%), Positives = 43/131 (32%), Gaps = 1/131 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVL-E 62 +++D + + + G E + S R D+ + + L Sbjct: 12 IVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCR 71 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 + +P+I ++ + + + G DD + KP + + V + +K + Sbjct: 72 WLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVKRT 131 Query: 123 NNRAETGPIRV 133 R I + Sbjct: 132 EERYSRESITL 142 >2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structure initiative; 1.80A {Bacteroides fragilis YCH46} Length = 140 Score = 45.0 bits (106), Expect = 1e-05 Identities = 19/121 (15%), Positives = 41/121 (33%), Gaps = 4/121 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLE- 62 ++DD V L + + +S + +V ++ E Sbjct: 8 IVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREENPEVVLLDMNFTSGINNGNEG 67 Query: 63 ---LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 L I R + +P++ + Y + + G D V KP ++++L + + Sbjct: 68 LFWLHEIKRQYRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAASQA 127 Query: 120 K 120 K Sbjct: 128 K 128 >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 = 44.8 bits (105), Expect = 1e-05 Identities = 21/115 (18%), Positives = 48/115 (41%), Gaps = 2/115 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + ++ ++F +G + + S ++ ++ L GK L Sbjct: 8 IVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGL--LL 65 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 R +R + V L+ ++ + + + G DD + KP + RE+ R + R Sbjct: 66 ARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR 120 >3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153 Score = 44.9 bits (106), Expect = 2e-05 Identities = 19/126 (15%), Positives = 39/126 (30%), Gaps = 4/126 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+D + ++ L +L + LQ A +V + + L Sbjct: 19 LVDSQEVILQRLQQLLSPLPYTLHFARD--ATQALQLLASREVDLVISAAHLPQMDGPTL 76 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSG-VDDVVNKPIHHREILARVAAIYRRLKV 121 I + I ++ P L+ + G + ++KP +E+L + Sbjct: 77 LARIHQQYPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQALEHQHS 136 Query: 122 SNNRAE 127 R Sbjct: 137 ERERLR 142 >2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima} Length = 142 Score = 44.7 bits (105), Expect = 2e-05 Identities = 19/117 (16%), Positives = 38/117 (32%), Gaps = 2/117 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++D+ + DG ++ +E RE + + + E + + Sbjct: 9 VVDESRITFLAVKNALEKDGFNVIWAK--NEQEAFTFLRREKIDLVFVDVFEGEESLNLI 66 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 RI + +S Y ++ +G D + KP +L RV I Sbjct: 67 RRIREEFPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISSTP 123 >3cu5_A Two component transcriptional regulator, ARAC family; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141 Score = 44.2 bits (104), Expect = 2e-05 Identities = 21/118 (17%), Positives = 43/118 (36%), Gaps = 2/118 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEW-LQSSAREDVSAIEAFLIGKGEKVLE 62 ++DD L +DG IA +S + + + +Q + + + + + +E Sbjct: 7 IVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIALKHPPNVLLTDVRMPRMDGIE 66 Query: 63 LPRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 L I + +I +S Y + V KPI EI+ + + + Sbjct: 67 LVDNILKLYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSIQTV 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 = 44.5 bits (105), Expect = 2e-05 Identities = 19/122 (15%), Positives = 45/122 (36%), Gaps = 6/122 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD++ ++ +F +G + + L +E + + G +E+ Sbjct: 8 IVDDQSGIRILLNEVFNKEGYQTFQAAN--GLQALDIVTKERPDLVLLDMKIPGMDGIEI 65 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 + ++ + +I ++ Y L + + G KP EI V L + Sbjct: 66 LKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKY---LPLK 122 Query: 123 NN 124 +N Sbjct: 123 SN 124 >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 = 44.3 bits (104), Expect = 2e-05 Identities = 19/118 (16%), Positives = 45/118 (38%), Gaps = 3/118 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + + G G + N + L ++ + + + + L Sbjct: 134 VVDDHPINRRLLADQLGSLGYQCKTAND--GVDALNVLSKNHIDIVLSDVNMPNMDGYRL 191 Query: 64 PRIIRAHS-QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 + IR +P+IG++ + +SG+D ++KP+ I + R++ Sbjct: 192 TQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVR 249 >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 = 44.4 bits (105), Expect = 2e-05 Identities = 15/118 (12%), Positives = 38/118 (32%), Gaps = 5/118 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D L + L G L + I + LE+ Sbjct: 6 IVEDNELNMKLFHDLLEAQGYETLQTRE--GLSALSIARENKPDLILMDIQLPEISGLEV 63 Query: 64 PRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + ++ + +P++ ++ + + G + ++KPI L + + R Sbjct: 64 TKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER 121 >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 = 44.0 bits (103), Expect = 2e-05 Identities = 16/119 (13%), Positives = 44/119 (36%), Gaps = 1/119 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +IDD + + L DG + +S + + + + + +++ Sbjct: 8 VIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDI 67 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKV 121 R I+ + +I ++ + L + G + + KP+ +++ + R K+ Sbjct: 68 LREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNAINRKKL 126 >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 = 43.9 bits (103), Expect = 3e-05 Identities = 19/116 (16%), Positives = 40/116 (34%), Gaps = 1/116 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD V+ + +G +++ S E R V + + V L Sbjct: 8 IVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVRNGV-LVTDLRMPDMSGVELL 66 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + +P I I+ + + ++ +G D + KP I+ + L Sbjct: 67 RNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHL 122 >3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.15A {Colwellia psychrerythraea 34H} Length = 135 Score = 43.8 bits (103), Expect = 3e-05 Identities = 22/121 (18%), Positives = 45/121 (37%), Gaps = 9/121 (7%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD L + + ++E F L + ++D+ ++ + +E+ Sbjct: 8 IVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLSLN-KQDIIILDLMMPDMDG--IEV 64 Query: 64 PRIIRA-HSQVPLIGISDY-----PSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 R + S LI IS Y S +T V + KPI+ + + ++ Sbjct: 65 IRHLAEHKSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSLSN 124 Query: 118 R 118 R Sbjct: 125 R 125 >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 = 43.0 bits (101), Expect = 5e-05 Identities = 26/125 (20%), Positives = 47/125 (37%), Gaps = 4/125 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 LIDD ++ G ++ F S E L + + + + + G L L Sbjct: 8 LIDDDRDLRKAMQQTLELAGFTVSSFAS--ATEALAGLSADFAGIVISDIRMPGMDGLAL 65 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARV-AAIYRRLKV 121 R I A +P+I ++ + + + G D + KP ++ A +R V Sbjct: 66 FRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLV 125 Query: 122 SNNRA 126 NR+ Sbjct: 126 MENRS 130 >2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143 Score = 43.3 bits (102), Expect = 5e-05 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 3/68 (4%) Query: 61 LELPRIIRAHS-QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 + L + I + + ++ I+ + + ++ F+ D + KP I+ + + Sbjct: 71 VLLAQNISQFAHKPFIVFITAWK--EHAVEAFELEAFDYILKPYQESRIINMLQKLTTAW 128 Query: 120 KVSNNRAE 127 + NN AE Sbjct: 129 EQQNNAAE 136 >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 = 42.9 bits (100), Expect = 6e-05 Identities = 19/116 (16%), Positives = 48/116 (41%), Gaps = 1/116 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GEKVLE 62 ++DD ++ D ++ + G S E ++ D+ ++ + G + LE Sbjct: 8 VVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLE 67 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + A +P++ ++ P + + S ++D + KP H ++ + + R Sbjct: 68 RIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVLAR 123 >2hqn_A Putative transcriptional regulator; phosporylation-independent response regulator, signaling protein; NMR {Helicobacter pylori J99} Length = 109 Score = 42.8 bits (100), Expect = 6e-05 Identities = 26/97 (26%), Positives = 48/97 (49%), Gaps = 1/97 (1%) Query: 122 SNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLF 181 +N E G + + D +G + + +L +L +R + V+K Q+ AI+ Sbjct: 3 GSNVIEIGDLTISPDEEKIIYKGREVEVKGKPFEVLTHLARHRDQIVSKEQLLDAIWEEP 62 Query: 182 DEAVEENVVESHISKLRKKLRNKLGFDPVDSKRFLGY 218 + V NV+E I+++R+K+ LG V++ R GY Sbjct: 63 EM-VTPNVIEVAINQIRQKMDKPLGISTVETVRRRGY 98 >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 = 42.2 bits (99), Expect = 8e-05 Identities = 21/117 (17%), Positives = 46/117 (39%), Gaps = 1/117 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + ++ G++ F + +S DV + + G + + L Sbjct: 8 VVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTPDVLLSDIRMPG-MDGLALL 66 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLK 120 +I + H +P+I ++ + L + + G D + KP E +A V + Sbjct: 67 KQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQ 123 >3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137 Score = 42.2 bits (99), Expect = 9e-05 Identities = 19/116 (16%), Positives = 43/116 (37%), Gaps = 3/116 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D ++ + + + E E L DV + + G LE+ Sbjct: 12 IVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFGLHAPDVIITDIRMPKLGG--LEM 69 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 I+A ++ +I IS + ++ + + GV + KPI ++ + Sbjct: 70 LDRIKAGGAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHI 125 >3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative; 2.04A {Staphylococcus aureus} Length = 133 Score = 42.2 bits (99), Expect = 9e-05 Identities = 20/120 (16%), Positives = 49/120 (40%), Gaps = 7/120 (5%) Query: 3 VLIDDRALVKDG---YIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGK-GE 58 ++ +D+ +++ I L GD + + N L+ + ++ +V ++ + G G Sbjct: 7 IIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIEEY-NPNVVILDIEMPGMTGL 65 Query: 59 KVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 +VL I + H + +I ++ + + VD V K E++ + + Sbjct: 66 EVLA--EIRKKHLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINKVNNG 123 >2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154 Score = 42.3 bits (99), Expect = 1e-04 Identities = 18/120 (15%), Positives = 46/120 (38%), Gaps = 6/120 (5%) Query: 3 VLIDDRALVKDGYIALFGD--DGVSLEGF-NSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 +++DD L++ G L G+ +EG + +L++ D+ ++ L + Sbjct: 7 LIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNL--PDAE 64 Query: 60 VLELPRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 ++ ++ + IS + ++G D + K + ++ V+ I Sbjct: 65 AIDGLVRLKRFDPSNAVALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLILEG 124 >2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A Length = 137 Score = 41.7 bits (97), Expect = 1e-04 Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 7/120 (5%) Query: 1 MFVLI-DDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEK 59 M VL+ + +++ G + SLE E+L D+ ++ Sbjct: 19 MRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMDIRNYDL-----VMVSDKNA 73 Query: 60 VLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHH-REILARVAAIYRR 118 + + RI HS + ++ SD P+ + + F+ G DD + KP + ++AR+ A R Sbjct: 74 LSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARLRF 133 >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 = 41.5 bits (98), Expect = 1e-04 Identities = 9/57 (15%), Positives = 26/57 (45%), Gaps = 3/57 (5%) Query: 65 RIIRAHS---QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + +R+ S ++P+I I+ + +GV++ + KP + + ++ + Sbjct: 71 KKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVLGT 127 >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 = 41.2 bits (96), Expect = 2e-04 Identities = 14/124 (11%), Positives = 46/124 (37%), Gaps = 8/124 (6%) Query: 4 LIDDRALVKDGYIALFGDDG-----VSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGE 58 +++D + ++ + +G ++ +G + + + L S + Sbjct: 7 VVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMD-VQMPKV 65 Query: 59 KVLELPRIIRAH--SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIY 116 L ++IR P++ ++ + + +SG++ ++KPI ++ + Sbjct: 66 DGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFC 125 Query: 117 RRLK 120 + Sbjct: 126 AAYQ 129 >2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92, PSI-2; 2.10A {Neptuniibacter caesariensis} Length = 154 Score = 41.2 bits (96), Expect = 2e-04 Identities = 21/127 (16%), Positives = 46/127 (36%), Gaps = 4/127 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+DD + + L G ++ F S + + + + + L Sbjct: 12 LVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTSVQLVISD-MRMPEMGGEVFL 70 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSG-VDDVVNKPIHHREILARVAAI--YRRLK 120 ++ +++ + + IS Y Q T+D + G + + KP ++ V L+ Sbjct: 71 EQVAKSYPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQLAFLR 130 Query: 121 VSNNRAE 127 N R + Sbjct: 131 EENLRLQ 137 >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 = 41.0 bits (96), Expect = 2e-04 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 2/60 (3%) Query: 61 LELPRIIRAH--SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 L + IRA Q +I ++ + T + G + KP + + +Y + Sbjct: 64 LAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK 123 >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 = 40.7 bits (95), Expect = 3e-04 Identities = 16/65 (24%), Positives = 30/65 (46%) Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 ++ + P++ ++ + + G DD + KP RE+ ARV AI RR ++ Sbjct: 66 CKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRRSEIR 125 Query: 123 NNRAE 127 +E Sbjct: 126 APSSE 130 >3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143 Score = 40.4 bits (95), Expect = 3e-04 Identities = 24/129 (18%), Positives = 46/129 (35%), Gaps = 25/129 (19%) Query: 4 LIDD---------RALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLI 54 + DD R L K G+ L + E+ L + A ED A+ L Sbjct: 19 VADDHEANRMVLQRLLEKAGHKVLCVNGA-----------EQVLDAMAEEDYDAVIVDLH 67 Query: 55 GKGEKVLELPRIIRAHS-----QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREIL 109 G L++ + +R P++ +S + + +G + KP+ ++L Sbjct: 68 MPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLL 127 Query: 110 ARVAAIYRR 118 +A + Sbjct: 128 DTLADLAVS 136 >3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116 Score = 40.4 bits (94), Expect = 4e-04 Identities = 19/113 (16%), Positives = 45/113 (39%), Gaps = 5/113 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD +++ ++G ++ + EE L+ + + + G LE+ Sbjct: 6 VVDDEPNIRELLKEELQEEGYEIDTAEN--GEEALKKFFSGNYDLVILDIEMPGISGLEV 63 Query: 64 PRIIRAHSQ-VPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAI 115 IR + +I ++ Y ++ D D+ V K + E+ +V + Sbjct: 64 AGEIRKKKKDAKIILLTAYSHYRS--DMSSWAADEYVVKSFNFDELKEKVKKL 114 >1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149 Score = 40.0 bits (93), Expect = 4e-04 Identities = 7/61 (11%), Positives = 26/61 (42%), Gaps = 3/61 (4%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 E+ I+ + ++P++ ++ + + ++ V+ + K + +++ V I Sbjct: 77 REVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIES 136 Query: 118 R 118 Sbjct: 137 F 137 >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 = 40.3 bits (94), Expect = 4e-04 Identities = 7/55 (12%), Positives = 20/55 (36%) Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 + I++ +I S ++ +G D + KP ++ + + + Sbjct: 66 IKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK 120 >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 = 39.7 bits (92), Expect = 5e-04 Identities = 16/135 (11%), Positives = 51/135 (37%), Gaps = 16/135 (11%) Query: 3 VLIDD---------RALVKDGYIA--LFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEA 51 V+I+D + + + G + DG S + + + S+ R + ++ Sbjct: 8 VMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDL 67 Query: 52 FLIGKGEKVLELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREI 108 L +++ ++++ + + P++ ++ + +D G + + KP+++ Sbjct: 68 NLPD--MTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENF 125 Query: 109 LARVAAIYRRLKVSN 123 + + V Sbjct: 126 ANAIRQLGLFFSVMQ 140 >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 = 39.9 bits (93), Expect = 5e-04 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 3/61 (4%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 E+ I++ ++P++ +S + +D V+ + K + ++ V I Sbjct: 71 REVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEE 130 Query: 118 R 118 Sbjct: 131 F 131 >3f6c_A Positive transcription regulator EVGA; structural genomics, , PSI-2, protein structure initiative; 1.45A {Escherichia coli k-12} Length = 134 Score = 39.7 bits (93), Expect = 5e-04 Identities = 18/117 (15%), Positives = 38/117 (32%), Gaps = 2/117 (1%) Query: 3 VLIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLE 62 ++IDD L L + + + + E +Q + + G ++ Sbjct: 5 IIIDDHPLAIAAIRNLLIKNDIEILAELT-EGGSAVQRVETLKPDIVIIDVDIPGVNGIQ 63 Query: 63 LPRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + +R +I +S D+G + V+K I+A + A Sbjct: 64 VLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNG 120 >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 = 39.5 bits (92), Expect = 6e-04 Identities = 16/117 (13%), Positives = 33/117 (28%), Gaps = 1/117 (0%) Query: 3 VLIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLE 62 V+ DD L ++G + G + + L+ G + Sbjct: 19 VVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQ 78 Query: 63 LPRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + +R+ ++ IS + G + K EI+ V + Sbjct: 79 VAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDCAKG 135 >3lte_A Response regulator; structural genomics, PSI, protein structure initiative, nysgrc, NEW YORK structural genomix research consortium; 2.00A {Bermanella marisrubri} Length = 132 Score = 39.6 bits (93), Expect = 6e-04 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 2/60 (3%) Query: 61 LELPRIIRAH--SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 L++ R +R + + P I + G DD + KP + +L R+ + Sbjct: 66 LDVIRSLRQNKVANQPKILVVSGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLVNE 125 >3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133 Score = 39.6 bits (93), Expect = 6e-04 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 4/61 (6%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 L R+ +P+I +S Y + +T D + KP+ ++A++ A+ Sbjct: 63 YALCGHFRSEPTLKHIPVIFVSGY-APRTEGPADQPVPDAYLVKPVKPPVLIAQLHALLA 121 Query: 118 R 118 R Sbjct: 122 R 122 >3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12} Length = 130 Score = 39.2 bits (91), Expect = 7e-04 Identities = 22/117 (18%), Positives = 40/117 (34%), Gaps = 4/117 (3%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + + + F G + L D+ + + L+L Sbjct: 12 IVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLGGFTPDLMICD--IAMPRMNGLKL 69 Query: 64 PRIIRAH-SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREIL-ARVAAIYRR 118 IR Q P++ IS ++ GV+DV+ KP+ L V A Sbjct: 70 LEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACLYP 126 >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 = 39.2 bits (91), Expect = 7e-04 Identities = 6/61 (9%), Positives = 23/61 (37%), Gaps = 3/61 (4%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 E+ + I+ ++P++ ++ + + + + + KP+ + V + Sbjct: 78 REVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIK 137 Query: 118 R 118 Sbjct: 138 Y 138 >3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP} Length = 153 Score = 38.8 bits (90), Expect = 9e-04 Identities = 22/116 (18%), Positives = 40/116 (34%), Gaps = 1/116 (0%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+DD +V++GY L + + E + + L G +E Sbjct: 10 LVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEA 69 Query: 64 PRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 R IR ++ + + L F++G V K E++ + AI Sbjct: 70 TRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAG 125 >3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140 Score = 38.5 bits (89), Expect = 0.001 Identities = 12/121 (9%), Positives = 36/121 (29%), Gaps = 6/121 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 + +D + + G + +S + ++ + + L Sbjct: 11 ICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVARRPYAAMTVDLN--LPDQDGVSL 68 Query: 64 PRIIRAHSQ---VPLIGISDYPSL-QTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRL 119 R +R S+ + ++ +S + + V + KPI ++ + + Sbjct: 69 IRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAIDNM 128 Query: 120 K 120 Sbjct: 129 A 129 >2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119 Score = 37.8 bits (87), Expect = 0.002 Identities = 12/112 (10%), Positives = 31/112 (27%), Gaps = 2/112 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+++ + G + L I + L L Sbjct: 6 LLEEEDEAATVVCEMLTAAGFKVIWLVD--GSTALDQLDLLQPIVILMAWPPPDQSCLLL 63 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAI 115 + +R H P + + + +++KP+ + +L + + Sbjct: 64 LQHLREHQADPHPPLVLFLGEPPVDPLLTAQASAILSKPLDPQLLLTTLQGL 115 >2hwv_A DNA-binding response regulator VICR; essential response regulator, C-terminal domain, DNA- binding domain, transcription; 1.90A {Enterococcus faecalis V583} Length = 121 Score = 37.8 bits (87), Expect = 0.002 Identities = 20/100 (20%), Positives = 45/100 (45%), Gaps = 2/100 (2%) Query: 122 SNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLF 181 + G + + D +GE L RE +L YL + G+ + + + ++G + Sbjct: 17 RGSHMTIGDLTIHPDAYMVSKRGEKIELTHREFELLYYLAKHIGQVMTREHLLQTVWG-Y 75 Query: 182 DEAVEENVVESHISKLRKKLRNKLG-FDPVDSKRFLGYSI 220 D + V+ + +LR+K+ + + ++R +GY + Sbjct: 76 DYFGDVRTVDVTVRRLREKIEDSPSHPTYLVTRRGVGYYL 115 >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 = 37.7 bits (87), Expect = 0.002 Identities = 15/118 (12%), Positives = 40/118 (33%), Gaps = 5/118 (4%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++ + + G +++ + R D+ + A + G+ + Sbjct: 10 IVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDL-VVLAVDLSAGQNGYLI 68 Query: 64 PRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 ++ VP++ I P + D+ V KP+ +++ R A+ Sbjct: 69 CGKLKKDDDLKNVPIVIIG-NPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALIGF 125 >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 = 37.3 bits (86), Expect = 0.003 Identities = 18/116 (15%), Positives = 42/116 (36%), Gaps = 3/116 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGF-NSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLE 62 L DD A++ + + D G + + + E L+S A D + + Sbjct: 10 LADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDGWQV 69 Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 +P++ IS + +L+ + ++ KP +++ V+ + Sbjct: 70 ARVAREIDPNMPIVYISGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQLLNA 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 = 37.3 bits (86), Expect = 0.003 Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 3/61 (4%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYR 117 L L R + +P+I +S F +G +D + K E++AR+ R Sbjct: 79 LTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRYHSR 138 Query: 118 R 118 Sbjct: 139 S 139 >3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Length = 127 Score = 37.2 bits (86), Expect = 0.003 Identities = 18/115 (15%), Positives = 36/115 (31%), Gaps = 6/115 (5%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 +++D + + L G + S S+ D I+ L L L Sbjct: 8 IVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMSTRGYDAVFIDLNL--PDTSGLAL 65 Query: 64 PRIIRA---HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAI 115 + +RA + +S + + D + KPI + + +I Sbjct: 66 VKQLRALPMEKTSKFVAVSGFAKNDLGKEA-CELFDFYLEKPIDIASLEPILQSI 119 >3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140 Score = 37.3 bits (86), Expect = 0.003 Identities = 16/120 (13%), Positives = 37/120 (30%), Gaps = 9/120 (7%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 + +D + + + + + LQ+ I + LE Sbjct: 15 IAEDNDICRLVAAKALEKCTNDITVVTN--GLQALQAYQNRQFDVIIMDIQMPVMDGLEA 72 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFD-----SGVDDVVNKPIHHREILARVAAIYRR 118 IR + + + T D D + +D+ V+KP++ ++ V + Sbjct: 73 VSEIRNYERTH--NTKRASIIAITADTIDDDRPGAELDEYVSKPLNPNQLRDVVLTCHSE 130 >1dcf_A ETR1 protein; beta-alpha five sandwich; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136 Score = 36.9 bits (85), Expect = 0.004 Identities = 10/49 (20%), Positives = 19/49 (38%) Query: 70 HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 H + L+ +S T G+D V+ KP+ I ++ + Sbjct: 81 HQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEP 129 >3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151 Score = 36.6 bits (84), Expect = 0.004 Identities = 19/125 (15%), Positives = 43/125 (34%), Gaps = 2/125 (1%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+DD + + D + E ++ S V + + E + Sbjct: 9 LVDDDYSLLNTLKRNLSFDFEVTTCESGPEALACIKKSDPFSV-IMVDMRMPGMEGTEVI 67 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLDFFDSG-VDDVVNKPIHHREILARVAAIYRRLKVS 122 + + ++ L T ++ + G V +NKP +I A + A ++ + Sbjct: 68 QKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQYDLV 127 Query: 123 NNRAE 127 ++ E Sbjct: 128 TSKEE 132 >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 = 36.4 bits (84), Expect = 0.005 Identities = 19/122 (15%), Positives = 43/122 (35%), Gaps = 9/122 (7%) Query: 4 LIDDRALVKDG---YIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKV 60 ++DD A+++ +I D V + N E + L + D+ ++ + Sbjct: 18 IVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEM--PVMDG 75 Query: 61 LELPRIIRAHSQ--VPLIGISDYPSLQTTLDFFDSGVDDVVNKPI--HHREILARVAAIY 116 +E R + ++ + ++ + G D VV KP ++ + Sbjct: 76 MEFLRHAKLKTRAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTVSHDLEEKTGGEL 135 Query: 117 RR 118 R Sbjct: 136 AR 137 >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 = 36.3 bits (83), Expect = 0.005 Identities = 21/131 (16%), Positives = 42/131 (32%), Gaps = 12/131 (9%) Query: 61 LELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAA--- 114 + R ++ +P++ I+ + +SG D + KPI + ARV + Sbjct: 61 FTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTR 120 Query: 115 ---IYRRLKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRER---RILEYLMANRGKRV 168 + L+ + + R + G V + ER R+ L + Sbjct: 121 FKLVIDELRQREASGRRMGVIAGAAARLDGLGGRVLIVDDNERQAQRVAAELGVEHRPVI 180 Query: 169 AKTQIFSAIYG 179 + I Sbjct: 181 ESDPEKAKISA 191 >2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Length = 143 Score = 36.1 bits (83), Expect = 0.007 Identities = 12/123 (9%), Positives = 38/123 (30%), Gaps = 9/123 (7%) Query: 4 LIDDRALVKDGYIALFGDDGVSLE------GFNSLEFEEWLQSSAREDVSAIEAFLIGKG 57 ++D + +F ++ G +L+ + I + Sbjct: 12 YLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPKLILLDINIPK 71 Query: 58 EKVLELPRIIRAH---SQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAA 114 +E + +R + + + ++ + + L F + + KP+ + E + Sbjct: 72 MNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWI 131 Query: 115 IYR 117 + Sbjct: 132 LQS 134 >1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196 Score = 36.0 bits (82), Expect = 0.008 Identities = 7/58 (12%), Positives = 19/58 (32%) Query: 61 LELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRR 118 + + L+ + +Y S + V+ +P+ +L + + R Sbjct: 68 EIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRI 125 >3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} Length = 394 Score = 35.8 bits (82), Expect = 0.008 Identities = 18/103 (17%), Positives = 35/103 (33%), Gaps = 2/103 (1%) Query: 61 LELPRIIRA-HSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREIL-ARVAAIYRR 118 LEL R IR S+ P+I +S + ++ G D + KP+ +L V R Sbjct: 65 LELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRALDR 124 Query: 119 LKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLM 161 + ++ + R++ ++ Sbjct: 125 AYLRVENQRYRDKLEAANRELQASLNLLQEDQNAGRQVQMNML 167 >2jk1_A HUPR, hydrogenase transcriptional regulatory protein HUPR1; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139 Score = 35.8 bits (82), Expect = 0.009 Identities = 20/116 (17%), Positives = 37/116 (31%), Gaps = 3/116 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 L+DD DD L + L+ + + I + V L Sbjct: 6 LVDDEPHSLAAMKLALEDDFDVLTAQGAEAAIAILEEEWVQVI--ICDQRMPGRTGVDFL 63 Query: 64 PRIIRAHSQVPLIGISDYPSLQTTLD-FFDSGVDDVVNKPIHHREILARVAAIYRR 118 + + I I+ Y + + D+G+ + KP H ++L+ R Sbjct: 64 TEVRERWPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAARM 119 >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 = 33.7 bits (77), Expect = 0.039 Identities = 18/129 (13%), Positives = 40/129 (31%), Gaps = 3/129 (2%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAREDVSAIEAFLIGKGEKVLEL 63 ++DD + A+ ++G + +L E + I + + Sbjct: 5 VVDDEESITSSLSAILEEEGYHPDTAKTLR--EAEKKIKELFFPVIVLDVWMPDGDGVNF 62 Query: 64 PRIIRAHS-QVPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKVS 122 I+ +S +I I+ + S+ T + G + + KP L + + Sbjct: 63 IDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKK 122 Query: 123 NNRAETGPI 131 E Sbjct: 123 APPQEEIEF 131 >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 = 32.6 bits (74), Expect = 0.068 Identities = 14/123 (11%), Positives = 35/123 (28%), Gaps = 7/123 (5%) Query: 4 LIDDRALVKDGYIALFGDDGVSLEGFNSLEFEEWLQSSAR-EDVSAIEAFLIGKGEKVLE 62 L++D G + S + Q ++ + + Sbjct: 20 LVEDEPSHATLIQYHLNQLGAEVTVHPS--GSAFFQHRSQLSTCDLLIVSDQLVDLSIFS 77 Query: 63 LPRIIRAHSQ-VPLIGISDYPSLQTTLDFFDSGVDDVVNKPIHHREILARVAAIYRRLKV 121 L I++ ++ ++ ++ L + KP E+ A + + V Sbjct: 78 LLDIVKEQTKQPSVLILTTGRH---ELIESSEHNLSYLQKPFAISELRAAIDYHKPSMGV 134 Query: 122 SNN 124 + N Sbjct: 135 TMN 137 >3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein structure initiative, structural genomics; 2.59A {Cytophaga hutchinsonii atcc 33406} Length = 146 Score = 32.5 bits (73), Expect = 0.077 Identities = 5/29 (17%), Positives = 9/29 (31%) Query: 90 FFDSGVDDVVNKPIHHREILARVAAIYRR 118 VD V+KP+ + + Sbjct: 111 EASDWVDYYVSKPLTANALNNLYNKVLNE 139 >2krf_A Transcriptional regulatory protein COMA; activator, competence, DNA-binding, transcription regulation component regulatory system; NMR {Bacillus subtilis} Length = 73 Score = 31.8 bits (73), Expect = 0.14 Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 10/65 (15%) Query: 137 GRDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISK 196 G Q E L RE IL+ + +G +I + L + +E ++ Sbjct: 1 GSHMSSQKEQDVLTPRECLILQEVE--KGFTNQ--EI-ADALHLS-----KRSIEYSLTS 50 Query: 197 LRKKL 201 + KL Sbjct: 51 IFNKL 55 >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 = 0.31 Identities = 23/103 (22%), Positives = 34/103 (33%), Gaps = 36/103 (34%) Query: 9 AL---VKDG----YIALFGDDGVSLEGFNSL----------------EFEEWLQSSARED 45 AL V +G A+FG G + + F L E L R Sbjct: 144 ALFRAVGEGNAQLV-AIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTT 202 Query: 46 VSAIEAFLIGKGEKV---LELPR-------IIRAHSQVPLIGI 78 + A + F +G + LE P ++ PLIG+ Sbjct: 203 LDAEKVF--TQGLNILEWLENPSNTPDKDYLLSIPISCPLIGV 243 >3c57_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Length = 95 Score = 29.1 bits (65), Expect = 0.81 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 10/64 (15%) Query: 138 RDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKL 197 R +Q + L +ER +L L G + + E V++++S+L Sbjct: 17 RGSHMQDPLSGLTDQERTLLGLLS--EGLTNKQIADRMFL--------AEKTVKNYVSRL 66 Query: 198 RKKL 201 KL Sbjct: 67 LAKL 70 >3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3cpw_Y* Length = 116 Score = 29.0 bits (65), Expect = 0.93 Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 20/65 (30%) Query: 138 RDPEVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKL 197 R+P ++G ++PL ++ MA++ + + F A YG Sbjct: 7 REPNLEGLMWPLGGQQTT-----MASKSGKTGSSGRFGARYG---------------RVS 46 Query: 198 RKKLR 202 R+++ Sbjct: 47 RRRVA 51 >1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Length = 82 Score = 28.5 bits (64), Expect = 1.3 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 10/57 (17%) Query: 145 EVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201 +V L RER IL+ + +G I + + E+ V+ H+ + KK+ Sbjct: 18 DVNQLTPRERDILKLIA--QGLPNK--MI-ARRLDI-----TESTVKVHVKHMLKKM 64 >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 = 28.4 bits (63), Expect = 1.4 Identities = 10/80 (12%), Positives = 27/80 (33%), Gaps = 5/80 (6%) Query: 63 LPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDVVNKP--IHHREILARVAAIYRRLK 120 + I++ +I S ++ +G D + + + ++ ++A + Sbjct: 44 IKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVNTAAVENPSLITQIAQTFGSQA 103 Query: 121 VSN---NRAETGPIRVFSDG 137 V + G VF+ Sbjct: 104 VVVAIDAKRVDGEFMVFTYS 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 = 28.0 bits (61), Expect = 1.8 Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 6/32 (18%) Query: 6 DDRALVK-DGYIALFGDD---GVSLEGFNSLE 33 + +AL K + L+ DD ++++ ++E Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKA--TME 47 >1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A {Escherichia coli} SCOP: b.80.6.1 PDB: 2zu0_A* Length = 435 Score = 27.7 bits (60), Expect = 2.0 Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 6/51 (11%) Query: 157 LEYLMANRG--KRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKL 205 + YL + RG ++ A+ I IY E E E ++ ++ +L Sbjct: 374 IFYLRS-RGINQQDAQQMI---IYAFAAELTEALRDEGLKQQVLARIGQRL 420 >2huj_A LIN2004 protein; hypothetical protein, structural genomics, PSI- 2, protein structure initiative, joint center for structural genomics, JCSG; 1.74A {Listeria innocua} SCOP: a.24.26.1 Length = 140 Score = 27.8 bits (62), Expect = 2.1 Identities = 8/87 (9%), Positives = 25/87 (28%), Gaps = 13/87 (14%) Query: 123 NNRAETGPIRVFSDGRDPEVQGEVFP--------LPRRERRILEYLMANRGKRVAKTQIF 174 N + + + + + ++ P + ++ R + + Q+ Sbjct: 33 NEKNWELYLSNREEEKPFDFYKDMKPFVDEAKRCADDFLELAIPWVNTERPPYLGELQLR 92 Query: 175 SAIYGLFDEAVEENVVESHISKLRKKL 201 A + V+ V + + K Sbjct: 93 QAC-----DNVQMTAVSAFNGRSFYKH 114 >1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Length = 79 Score = 27.0 bits (60), Expect = 3.3 Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 10/61 (16%) Query: 141 EVQGEVFPLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKK 200 +++ + L RER++L ++A + + + VE H + + K Sbjct: 9 DIRARLQTLSERERQVLSAVVAGLPNKSIAYDLD----------ISPRTVEVHRANVMAK 58 Query: 201 L 201 + Sbjct: 59 M 59 >1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Length = 99 Score = 27.1 bits (60), Expect = 3.6 Identities = 6/54 (11%), Positives = 11/54 (20%), Gaps = 10/54 (18%) Query: 148 PLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201 L +E +L ++ + S KL Sbjct: 34 RLSPKESEVLRLFAEGFLVTEIAKKLN----------RSIKTISSQKKSAMMKL 77 >2ijz_A Probable M18-family aminopeptidase 2; putative aminopeptidase 2, structural genomics, PSI, protein structure initiative; 3.00A {Pseudomonas aeruginosa} Length = 428 Score = 27.0 bits (59), Expect = 3.8 Identities = 25/174 (14%), Positives = 48/174 (27%), Gaps = 27/174 (15%) Query: 47 SAIEAFLIGKGEKVLELPRIIRAHSQVPLIGISDYPSL--QTTLDFFDSGVDDVVNKP-- 102 S++ A +G+ + R++ AH +D P L + + +G + + Sbjct: 58 SSLIAIRLGRRSPLESGFRLVGAH--------TDSPCLRVKPNPEIARNGFLQLGVEVYG 109 Query: 103 -IHHREILARVAAIYRRLKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRERRILEYLM 161 R ++ R+ RA D R + L R Sbjct: 110 GALFAPWFDRDLSLAGRVTF---RANGKLESRLVDFRKA--IAVIPNLNIHLNR-----A 159 Query: 162 ANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKLRNKLGFDPVDSKRF 215 AN G + I + L ++L + G + Sbjct: 160 ANEGWPINAQNELPPIIAQLAPGEAAD----FRLLLDEQLLREHGITADVVLDY 209 >2yxn_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, structural genomics, NPPSFA; HET: AZY; 1.80A {Escherichia coli str} PDB: 1wq3_A* 1wq4_A* 1x8x_A* 1vbn_A* 1vbm_A* Length = 322 Score = 26.3 bits (57), Expect = 5.4 Identities = 7/31 (22%), Positives = 14/31 (45%), Gaps = 2/31 (6%) Query: 179 GLFDEAVEENVVESHISKLRKKLRNKLGFDP 209 GL + +E + +++ + GFDP Sbjct: 14 GLVAQVTDEEALAERLAQ--GPIALVCGFDP 42 >2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Length = 432 Score = 26.3 bits (57), Expect = 5.5 Identities = 6/31 (19%), Positives = 14/31 (45%), Gaps = 2/31 (6%) Query: 179 GLFDEAVEENVVESHISKLRKKLRNKLGFDP 209 GL ++ + + + + + + GFDP Sbjct: 13 GLIAQSTDLDTLAAEAQR--GPMTVYAGFDP 41 >1ep3_A Dihydroorotate dehydrogenase B (PYRD subunit); heterotetramer, alpha-beta barrel, beta sandwich, FAD domain, alpha/beta NADP domain; HET: FMN FAD; 2.10A {Lactococcus lactis} SCOP: c.1.4.1 PDB: 1ep2_A* 1ep1_A* Length = 311 Score = 26.5 bits (58), Expect = 5.5 Identities = 11/72 (15%), Positives = 29/72 (40%), Gaps = 6/72 (8%) Query: 58 EKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDSGVDDV------VNKPIHHREILAR 111 L+L + +P+IG+ + Q L+ + +G V P +I+ + Sbjct: 227 PVALKLIHQVAQDVDIPIIGMGGVANAQDVLEMYMAGASAVAVGTANFADPFVCPKIIDK 286 Query: 112 VAAIYRRLKVSN 123 + + + ++ + Sbjct: 287 LPELMDQYRIES 298 >3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164 Score = 26.4 bits (57), Expect = 5.9 Identities = 4/21 (19%), Positives = 10/21 (47%) Query: 185 VEENVVESHISKLRKKLRNKL 205 +++ I ++RKK + Sbjct: 136 KNLKSIDNTIQRIRKKSEEWI 156 >2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Length = 91 Score = 26.3 bits (58), Expect = 6.0 Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 11/66 (16%) Query: 137 GRDPEVQGEVF-PLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHIS 195 G + + E++ L RE IL + +G +I ++ + V++H+S Sbjct: 17 GSHMKKRAELYEMLTEREMEILLLIA--KGYSNQ--EI-ASASHI-----TIKTVKTHVS 66 Query: 196 KLRKKL 201 + KL Sbjct: 67 NILSKL 72 >2hfi_A Hypothetical protein YPPE; YPPE_bacsu, GFT structural genomics, PSI, protein structure initiative, northeast structural genomics consortium; NMR {Bacillus subtilis} SCOP: a.24.26.1 PDB: 2im8_A Length = 131 Score = 26.3 bits (58), Expect = 6.1 Identities = 15/93 (16%), Positives = 29/93 (31%), Gaps = 13/93 (13%) Query: 117 RRLKVSNNRAETGPIRVFSDGRDPEVQGEVFP--------LPRRERRILEYLMANRGKRV 168 ++ + + + + P R LE + R K V Sbjct: 11 EQMIEVAEKGADRYQEGKNSNHSYDFFETIKPAVEENDELAARWAEGALELIKVRRPKYV 70 Query: 169 AKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201 K QI + + E V++S++ + KK Sbjct: 71 HKEQIEAVK-----DNFLELVLQSYVHHIHKKR 98 >3bld_A Queuine tRNA-ribosyltransferase; TGT, PREQ1, glycosyltransferase, metal-binding, queuosine biosynthesis, tRNA processing, zinc; HET: PRF; 1.19A {Zymomonas mobilis} PDB: 3bl3_A* 1ozq_A* 1ozm_A* 1r5y_A* 1enu_A* 1f3e_A* 1k4h_A* 1n2v_A* 1p0b_A* 1p0d_A 1p0e_A* 1pud_A 1q2r_A* 1q2s_A* 1q4w_A* 1q63_A* 1q65_A* 1q66_A* 1k4g_A* 1s38_A* ... Length = 386 Score = 26.2 bits (57), Expect = 6.8 Identities = 10/58 (17%), Positives = 20/58 (34%) Query: 96 DDVVNKPIHHREILARVAAIYRRLKVSNNRAETGPIRVFSDGRDPEVQGEVFPLPRRE 153 D+ P + + R K S + ++ + + QG VF R++ Sbjct: 156 DECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQ 213 >2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Length = 419 Score = 25.9 bits (56), Expect = 6.9 Identities = 7/31 (22%), Positives = 18/31 (58%), Gaps = 2/31 (6%) Query: 179 GLFDEAVEENVVESHISKLRKKLRNKLGFDP 209 GL ++ +E+ + +++ +++ GFDP Sbjct: 11 GLVNQTTDEDGLRKLLNE--ERVTLYCGFDP 39 >2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Length = 236 Score = 26.0 bits (56), Expect = 7.1 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 10/54 (18%) Query: 148 PLPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201 L RE L A++GK + + + V+ ++ K R KL Sbjct: 175 MLSPREMLCLV--WASKGKTAS--VTANLTG------INARTVQHYLDKARAKL 218 >2zkr_g 60S acidic ribosomal protein P0; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 317 Score = 25.6 bits (56), Expect = 8.4 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 6/53 (11%) Query: 161 MANRGKRVAKTQIFSAIYGLFDEA-----VE-ENVVESHISKLRKKLRNKLGF 207 M + K+ F I L D+ V +NV + ++R LR K Sbjct: 1 MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVV 53 >3mva_O Transcription termination factor, mitochondrial; all alpha-helix, protein-DNA, transcription factor, terminat mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O 3n7q_A* Length = 343 Score = 25.5 bits (55), Expect = 9.6 Identities = 9/58 (15%), Positives = 18/58 (31%), Gaps = 3/58 (5%) Query: 36 EWLQSSAREDVSAIEAFLIGKGEKVLELPRIIRAHSQVPLIGISDYPSLQTTLDFFDS 93 + + ++ FL+ KG + II + P +L D + Sbjct: 41 PGVFHRMITNEQDLKMFLLSKGASKEVIASIISRY---PRAITRTPENLSKRWDLWRK 95 >1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Length = 74 Score = 25.5 bits (56), Expect = 9.6 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 10/53 (18%) Query: 149 LPRRERRILEYLMANRGKRVAKTQIFSAIYGLFDEAVEENVVESHISKLRKKL 201 L +RER + E L+ + K +I ++ + E V +HIS +KL Sbjct: 12 LTKREREVFELLV--QDKTTK--EI-ASELFIS-----EKTVRNHISNAMQKL 54 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 0.321 0.140 0.404 Gapped Lambda K H 0.267 0.0499 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,022,495 Number of extensions: 94375 Number of successful extensions: 439 Number of sequences better than 10.0: 1 Number of HSP's gapped: 411 Number of HSP's successfully gapped: 143 Length of query: 223 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 134 Effective length of database: 3,535,514 Effective search space: 473758876 Effective search space used: 473758876 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.5 bits)