BLASTP 2.2.21 [Jun-14-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0002.0028.p (454 letters) Database: COGmodified 192,987 sequences; 59,019,183 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value RSc0506 [J] COG0042 tRNA-dihydrouridine synthase Rso Ralstonia s... 470 e-132 PA4852 [J] COG0042 tRNA-dihydrouridine synthase Pae Pseudomonas ... 434 e-121 STM3384 [J] COG0042 tRNA-dihydrouridine synthase Sty Salmonella ... 363 e-100 yhdG [J] COG0042 tRNA-dihydrouridine synthase Eco Escherichia co... 358 2e-98 ZyhdG [J] COG0042 tRNA-dihydrouridine synthase EcZ Escherichia c... 358 2e-98 >RSc0506 [J] COG0042 tRNA-dihydrouridine synthase Rso Ralstonia solanacearum Length = 356 Score = 470 bits (1209), Expect = e-132, Method: Compositional matrix adjust. Identities = 225/319 (70%), Positives = 262/319 (82%), Gaps = 2/319 (0%) Query: 1 VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 60 + IGP+ LRNN+FVAPMAGVTDRPFRQLCK+LGAGYAVSEM AS+ +LW SE+T RR NH Sbjct: 1 MQIGPHILRNNLFVAPMAGVTDRPFRQLCKRLGAGYAVSEMVASNAQLWKSERTMRRANH 60 Query: 61 DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120 GE+EP AVQIAGA+P+M+A+ A+YNVERGAQIIDINMGCP KKVCN GSALLQ+E L Sbjct: 61 TGEVEPIAVQIAGAEPMMMAEAARYNVERGAQIIDINMGCPAKKVCNVAAGSALLQNEPL 120 Query: 121 VARILDAVVSAVD--VPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYS 178 VARI++AVV AV VPVTLK RTGW+R ++NAL +A A+ AGI+MLT+HGRTRAD Y Sbjct: 121 VARIVEAVVGAVGDRVPVTLKIRTGWDREHRNALTVARIAQEAGISMLTVHGRTRADLYH 180 Query: 179 GEAEYETIAAVKAAVKMPVVANGDITTPEKAREVLRLTGADAVMVGRAAQGRPWIFREID 238 GEAEYETIAAVKA+V++PVVANGDI TP KAR VL +TGADA+M+GRAAQGRPW+FREI+ Sbjct: 181 GEAEYETIAAVKASVRIPVVANGDIGTPAKARHVLEVTGADAIMIGRAAQGRPWLFREIE 240 Query: 239 HFLRTGEHLPAPLVTEVAHLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGETFRR 298 HFL+TG LPAP V E+ +M+ HL+ HYAFYG+Y GVRTARKHI WY R L G FR Sbjct: 241 HFLKTGTLLPAPEVEEIRGIMNTHLEEHYAFYGEYTGVRTARKHIAWYTRGLAGANLFRH 300 Query: 299 SMNRIEDCGQQLQAVRQFL 317 MN IED QL AV F Sbjct: 301 RMNTIEDTAAQLAAVNAFF 319 >PA4852 [J] COG0042 tRNA-dihydrouridine synthase Pae Pseudomonas aeruginosa Length = 332 Score = 434 bits (1115), Expect = e-121, Method: Compositional matrix adjust. Identities = 213/335 (63%), Positives = 253/335 (75%), Gaps = 7/335 (2%) Query: 1 VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 60 V IGPY+L N + +APMAGVTDRPFRQLC++LGAG VSEM SD RLW+S K+ R+ H Sbjct: 4 VRIGPYTLPNRLILAPMAGVTDRPFRQLCRRLGAGMVVSEMVTSDVRLWNSRKSRLRLIH 63 Query: 61 DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120 DGE EP++VQIAG DP MLA+ A+ NVE GAQIIDINMGCP KKVCN GSALL+DE L Sbjct: 64 DGEDEPRSVQIAGGDPAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEAL 123 Query: 121 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 180 VA ILDAVV AVDVPVTLK RTGW+R N+N + +A AE AGI L +HGRTRAD Y+GE Sbjct: 124 VAEILDAVVRAVDVPVTLKIRTGWDRDNRNGVTVAKLAEQAGIQALAVHGRTRADLYTGE 183 Query: 181 AEYETIAAVKAAVKMPVVANGDITTPEKAREVLRLTGADAVMVGRAAQGRPWIFREIDHF 240 AEYETIAA+K AV +PV ANGDI +PEKAR+V+ TG DA+++GRAAQGRPWIFREIDH+ Sbjct: 184 AEYETIAAIKQAVSIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHY 243 Query: 241 LRTGEHLPAPLVTEVAHLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGETFRRSM 300 LRTGEHLPA + EV ++ EHL + FYG+ +GVR ARKH+GWY+ LPG FR Sbjct: 244 LRTGEHLPAAPLPEVQSILLEHLAELHLFYGEEMGVRIARKHVGWYLATLPGAREFRAQF 303 Query: 301 NRIEDCGQQLQAVRQFLFGGXGRTARQDNKGIGCA 335 NR++D Q +VRQF A + N G G A Sbjct: 304 NRLQDTDAQCASVRQFF-------AERQNNGTGVA 331 >STM3384 [J] COG0042 tRNA-dihydrouridine synthase Sty Salmonella typhimurium LT2 Length = 321 Score = 363 bits (933), Expect = e-100, Method: Compositional matrix adjust. Identities = 178/317 (56%), Positives = 226/317 (71%) Query: 1 VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 60 + IG Y LRN + APMAG+TDRPFR LC ++GAG VSEM +S+P++W S+K+ R+ H Sbjct: 1 MRIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVH 60 Query: 61 DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120 E + VQIAG+DPV +AD A+ NVE GAQIIDINMGCP KKV GSALLQ +L Sbjct: 61 VDEPGIRTVQIAGSDPVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDL 120 Query: 121 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 180 V IL VV+AVDVPVTLK RTGW ++N ++IA AE GI LT+HGRTRA ++GE Sbjct: 121 VKSILIGVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNGE 180 Query: 181 AEYETIAAVKAAVKMPVVANGDITTPEKAREVLRLTGADAVMVGRAAQGRPWIFREIDHF 240 AEY++I AVK V +P++ANGDIT P KAR VL TGADA+M+GRAAQGRPWIFREI H+ Sbjct: 181 AEYDSIRAVKQKVSIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHY 240 Query: 241 LRTGEHLPAPLVTEVAHLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGETFRRSM 300 L TGE LP + EV L+ H++ + FYG G R ARKH+ WY+++ + FRR+ Sbjct: 241 LDTGELLPPLPLAEVKRLLCTHVRELHDFYGQAKGYRIARKHVSWYLQEHAPDDQFRRTF 300 Query: 301 NRIEDCGQQLQAVRQFL 317 N IED +QL+A+ + Sbjct: 301 NAIEDASEQLEALEAYF 317 >yhdG [J] COG0042 tRNA-dihydrouridine synthase Eco Escherichia coli K12 Length = 321 Score = 358 bits (918), Expect = 2e-98, Method: Compositional matrix adjust. Identities = 177/317 (55%), Positives = 224/317 (70%) Query: 1 VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 60 + IG Y LRN + APMAG+TDRPFR LC ++GAG VSEM +S+P++W S+K+ R+ H Sbjct: 1 MRIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVH 60 Query: 61 DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120 E + VQIAG+DP +AD A+ NVE GAQIIDINMGCP KKV GSALLQ ++ Sbjct: 61 IDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDV 120 Query: 121 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 180 V IL VV+AVDVPVTLK RTGW ++N +IA AE GI LT+HGRTRA ++GE Sbjct: 121 VKSILTEVVNAVDVPVTLKIRTGWAPEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNGE 180 Query: 181 AEYETIAAVKAAVKMPVVANGDITTPEKAREVLRLTGADAVMVGRAAQGRPWIFREIDHF 240 AEY++I AVK V +PV+ANGDIT P KAR VL TGADA+M+GRAAQGRPWIFREI H+ Sbjct: 181 AEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHY 240 Query: 241 LRTGEHLPAPLVTEVAHLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGETFRRSM 300 L TGE LP + EV L+ H++ + FYG G R ARKH+ WY+++ + FRR+ Sbjct: 241 LDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTF 300 Query: 301 NRIEDCGQQLQAVRQFL 317 N IED +QL+A+ + Sbjct: 301 NAIEDASEQLEALEAYF 317 >ZyhdG [J] COG0042 tRNA-dihydrouridine synthase EcZ Escherichia coli O157:H7 EDL933 Length = 321 Score = 358 bits (918), Expect = 2e-98, Method: Compositional matrix adjust. Identities = 177/317 (55%), Positives = 224/317 (70%) Query: 1 VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 60 + IG Y LRN + APMAG+TDRPFR LC ++GAG VSEM +S+P++W S+K+ R+ H Sbjct: 1 MRIGQYQLRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEMMSSNPQVWESDKSRLRMVH 60 Query: 61 DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120 E + VQIAG+DP +AD A+ NVE GAQIIDINMGCP KKV GSALLQ ++ Sbjct: 61 IDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDV 120 Query: 121 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 180 V IL VV+AVDVPVTLK RTGW ++N +IA AE GI LT+HGRTRA ++GE Sbjct: 121 VKSILTEVVNAVDVPVTLKIRTGWAPEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNGE 180 Query: 181 AEYETIAAVKAAVKMPVVANGDITTPEKAREVLRLTGADAVMVGRAAQGRPWIFREIDHF 240 AEY++I AVK V +PV+ANGDIT P KAR VL TGADA+M+GRAAQGRPWIFREI H+ Sbjct: 181 AEYDSIRAVKQKVSIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHY 240 Query: 241 LRTGEHLPAPLVTEVAHLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGETFRRSM 300 L TGE LP + EV L+ H++ + FYG G R ARKH+ WY+++ + FRR+ Sbjct: 241 LDTGELLPPLPLAEVKRLLCAHVRELHDFYGPAKGYRIARKHVSWYLQEHAPNDQFRRTF 300 Query: 301 NRIEDCGQQLQAVRQFL 317 N IED +QL+A+ + Sbjct: 301 NAIEDASEQLEALEAYF 317