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= 0004.0105.p (303 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 15,459,386 sequences; 5,307,515,862 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|ZP_08273087.1| mRNA 3'-end processing factor [Oxalobacterace... 417 e-114 ref|YP_003775686.1| exonuclease of the beta-lactamase fold invol... 415 e-114 ref|YP_001020716.1| hypothetical protein Mpe_A1519 [Methylibium ... 380 e-103 gb|ADR58838.1| RNA processing exonuclease [Pseudomonas putida BI... 374 e-102 ref|YP_002946730.1| mRNA 3-end processing factor [Variovorax par... 374 e-102 >ref|ZP_08273087.1| mRNA 3'-end processing factor [Oxalobacteraceae bacterium IMCC9480] gb|EGF33432.1| mRNA 3'-end processing factor [Oxalobacteraceae bacterium IMCC9480] Length = 340 Score = 417 bits (1071), Expect = e-114, Method: Compositional matrix adjust. Identities = 203/329 (61%), Positives = 237/329 (72%), Gaps = 52/329 (15%) Query: 1 MSDMVVVRKEGLYCVPGDFHIDPWRPVDRAVITHAHADHARTGHGHYLATADGAGILRAR 60 M+D++V R EGLYCVPG F+IDPWR VDRAVITH HADH+RTGHGHYLATA GAGIL +R Sbjct: 1 MADLIVARPEGLYCVPGQFYIDPWRAVDRAVITHGHADHSRTGHGHYLATAAGAGILHSR 60 Query: 61 LGEIRLDALRYGESITHNGVALSLHPAGHVLGSAQLRMEHRGEVWVASGDYKLERDGTCA 120 LG+I L L YGE++ HNGV +SLHPAGHVLGSAQ+R+E+RGEVWVASGDYK+E D TCA Sbjct: 61 LGKINLQTLAYGETLLHNGVTISLHPAGHVLGSAQVRLEYRGEVWVASGDYKVEADATCA 120 Query: 121 PFESVRCDTFITESTFGMPIYRWQPQAEIFDDINAWWRRNAAEGRTSVLFCYAFGKAQRI 180 FE VRCDTFITESTFG+PIYRWQ Q EIFD+IN WWR NAA+GR SVLFCY+FGK QR+ Sbjct: 121 AFEPVRCDTFITESTFGLPIYRWQAQQEIFDEINQWWRDNAADGRASVLFCYSFGKTQRL 180 Query: 181 LHGLDPTIGSIVCHGAVTPLNALYREAGVALPPTLAVGDVEDKAVLRQALVLAPPSXA-- 238 L G+DP+IG I+CH A PLN +YREAG+ALP +L V +V DKA L++ALVLAPP+ A Sbjct: 181 LSGVDPSIGPIICHSAAEPLNRVYREAGIALPDSLLVTEVADKADLKRALVLAPPATAGS 240 Query: 239 --------------------------------------------------SGAARIIVTH 248 +GA R+IVTH Sbjct: 241 PWLKRFGDYSDAFASGWMLLRGARRRRAVDRGFVLSDHADWPGLMQAIKETGAQRVIVTH 300 Query: 249 GQIPIMVRWLQQNGLDAGAFDTEYGGEEE 277 GQ+ +MVRWLQQNGL AGAF TEYG EE+ Sbjct: 301 GQVAVMVRWLQQNGLQAGAFQTEYGIEED 329 >ref|YP_003775686.1| exonuclease of the beta-lactamase fold involved in RNA processing protein [Herbaspirillum seropedicae SmR1] gb|ADJ63778.1| exonuclease of the beta-lactamase fold involved in RNA processing protein [Herbaspirillum seropedicae SmR1] Length = 355 Score = 415 bits (1066), Expect = e-114, Method: Compositional matrix adjust. Identities = 216/339 (63%), Positives = 233/339 (68%), Gaps = 64/339 (18%) Query: 1 MSDMVVVRKEGLYCVPGDFHIDPWRPVDRAVITHAHADHARTGHGHYLATADGAGILRAR 60 M DMVVVRKEGLYCVPGDF+IDPWRPV RAVITHAHADHAR GH HYLA A GA ILRAR Sbjct: 1 MQDMVVVRKEGLYCVPGDFYIDPWRPVARAVITHAHADHARVGHAHYLAAAPGADILRAR 60 Query: 61 LG-EIRLDALRYGESITHNGVALSLHPAGHVLGSAQLRMEHRGEVWVASGDYKLERDGTC 119 LG +I LD L YG S+THNGV LSLHPAGHVLGSAQLRMEH G+VWVASGDYKLE DGTC Sbjct: 61 LGADIALDTLAYGASLTHNGVRLSLHPAGHVLGSAQLRMEHEGQVWVASGDYKLEADGTC 120 Query: 120 APFESVRCDTFITESTFGMPIYRWQPQAEIFDDINAWWRRNAAEGRTSVLFCYAFGKAQR 179 APFE VRC TFITESTFGMPIYRWQPQAEIF++INAWWR NAA+GR SVLFCYAFGKAQR Sbjct: 121 APFEPVRCHTFITESTFGMPIYRWQPQAEIFEEINAWWRANAAQGRASVLFCYAFGKAQR 180 Query: 180 ILHGLDPTIGSIVCHGAVTPLNALYREAGVALPPTLAV-----------GDVEDKAVLRQ 228 ILHG+D +IG I+CHGAV PLN LYR+ GVALP T V G + Sbjct: 181 ILHGIDASIGPIICHGAVAPLNRLYRQEGVALPETQTVNQGSPGSKSDGGKRSPSSAYAG 240 Query: 229 ALVLAPPS---------------------------------------------------- 236 +LV+APPS Sbjct: 241 SLVIAPPSAAGSPWMRRFGDYSDAFASGWMRLRGTRRRRGVDRGFVLSDHADWPALQQAI 300 Query: 237 XASGAARIIVTHGQIPIMVRWLQQNGLDAGAFDTEYGGE 275 A+ A RIIVTHGQ+ MVRWL+QNGLDAGAF TEYG E Sbjct: 301 AATQAERIIVTHGQVATMVRWLRQNGLDAGAFATEYGDE 339 >ref|YP_001020716.1| hypothetical protein Mpe_A1519 [Methylibium petroleiphilum PM1] gb|ABM94481.1| conserved hypothetical protein [Methylibium petroleiphilum PM1] Length = 340 Score = 380 bits (976), Expect = e-103, Method: Compositional matrix adjust. Identities = 191/330 (57%), Positives = 223/330 (67%), Gaps = 52/330 (15%) Query: 1 MSDMVVVRKEGLYCVPGDFHIDPWRPVDRAVITHAHADHARTGHGHYLATADGAGILRAR 60 MSD+VVVRKEGLYC GDF+IDPWRPV RAV+THAHADHAR GHG YLA GA ++R R Sbjct: 1 MSDLVVVRKEGLYCAAGDFYIDPWRPVARAVLTHAHADHARPGHGRYLAARAGATLVRTR 60 Query: 61 LGEIRLDALRYGESITHNGVALSLHPAGHVLGSAQLRMEHRGEVWVASGDYKLERDGTCA 120 LG++ LD L YGE ITH+GV LSLHPAGHVLGSAQ+R+EHRGEVWV SGDYKL D +CA Sbjct: 61 LGDVGLDTLEYGERITHHGVTLSLHPAGHVLGSAQVRLEHRGEVWVVSGDYKLAPDASCA 120 Query: 121 PFESVRCDTFITESTFGMPIYRWQPQAEIFDDINAWWRRNAAEGRTSVLFCYAFGKAQRI 180 PFE +RCDTF+TESTFG+PIYRW P A++FD + WWR NA G+ SVL+CYA GKAQR+ Sbjct: 121 PFEPLRCDTFVTESTFGLPIYRWDPPAQVFDGVEHWWRDNADAGQASVLYCYALGKAQRV 180 Query: 181 LHGLDPTIGSIVCHGAVTPLNALYREAGVALPPTLAVGDVEDKAVLRQALVLAPPSX--- 237 L G+D +IG IVCHGAV LN YR AGVALPPT+ V V D LR+ALVLAPPS Sbjct: 181 LLGVDASIGPIVCHGAVQTLNDAYRAAGVALPPTITVDQVGDPVDLRRALVLAPPSAAGS 240 Query: 238 -------------------------------------------------ASGAARIIVTH 248 A+GA RI+VTH Sbjct: 241 PWLKRFGEFHDAFASGWMRLRGTRRRRGVDRGFVLSDHADWPALLEAIGATGAGRIVVTH 300 Query: 249 GQIPIMVRWLQQNGLDAGAFDTEYGGEEEV 278 G+ ++RWL++ GLDA AF TEYG E+E Sbjct: 301 GETGPLIRWLREQGLDAAAFQTEYGDEDET 330 >gb|ADR58838.1| RNA processing exonuclease [Pseudomonas putida BIRD-1] Length = 338 Score = 374 bits (961), Expect = e-102, Method: Compositional matrix adjust. Identities = 190/332 (57%), Positives = 226/332 (68%), Gaps = 54/332 (16%) Query: 3 DMVVVRKEGLYCVPGDFHIDPWRPVDRAVITHAHADHARTGHGHYLATADGAGILRARLG 62 D+V+ R EGLYC PGDF+IDPWRPVDRAVITH H DHARTG+GHYL + GAGILR+RLG Sbjct: 2 DLVIARPEGLYCPPGDFYIDPWRPVDRAVITHGHGDHARTGNGHYLTASPGAGILRSRLG 61 Query: 63 E-IRLDALRYGESITHNGVALSLHPAGHVLGSAQLRMEHRGEVWVASGDYKLERDGTCAP 121 + I L L YGE + H+GV LSLHPAGHVLGSAQ+R+E+RGEVWVASGDYK+E DGTC P Sbjct: 62 QDINLQTLPYGERLPHHGVTLSLHPAGHVLGSAQVRLEYRGEVWVASGDYKVEPDGTCTP 121 Query: 122 FESVRCDTFITESTFGMPIYRWQPQAEIFDDINAWWRRNAAEGRTSVLFCYAFGKAQRIL 181 FE V C TFITESTFG+PIYRW Q+EIF INAWWR N +G+ SVLFCYAFGKAQRIL Sbjct: 122 FEPVACHTFITESTFGLPIYRWPSQSEIFASINAWWRANREQGKASVLFCYAFGKAQRIL 181 Query: 182 HGLDPTIGSIVCHGAVTPLNALYREAGVALPPTLAVGDV-EDKAVLRQALVLAPPSXA-- 238 HGLD +IG I+ HGA+ PLN +YR+AG+ LP T GD+ + +LRQALVLAPPS Sbjct: 182 HGLDASIGPILVHGAMEPLNRVYRDAGIHLPETRYAGDIPRNDPLLRQALVLAPPSAGGS 241 Query: 239 --------------------------------------------------SGAARIIVTH 248 +GA R++VTH Sbjct: 242 SWMRRFGDYSDAFASGWMLLRGARRRRGVDRGFVLSDHADWPGLLWAIGQTGAQRVMVTH 301 Query: 249 GQIPIMVRWLQQNGLDAGAFDTEYGGEEEVEN 280 G + ++VR+L + GLDA AF TEYG E++V N Sbjct: 302 GSVEVLVRYLTEQGLDARAFVTEYGDEDDVPN 333 >ref|YP_002946730.1| mRNA 3-end processing factor [Variovorax paradoxus S110] gb|ACS21464.1| putative mRNA 3-end processing factor [Variovorax paradoxus S110] Length = 375 Score = 374 bits (961), Expect = e-102, Method: Compositional matrix adjust. Identities = 195/331 (58%), Positives = 224/331 (67%), Gaps = 54/331 (16%) Query: 4 MVVVRKEGLYCVPGDFHIDPWRPVDRAVITHAHADHARTGHGHYLATADGAGILRARLG- 62 +VV R EGLYC PGDF+IDPWRPV RAVITHAH+DHAR GHGHYLA D AG LR RLG Sbjct: 9 LVVARPEGLYCPPGDFYIDPWRPVARAVITHAHSDHARAGHGHYLAHTDSAGTLRTRLGG 68 Query: 63 EIRLDALRYGESITHNGVALSLHPAGHVLGSAQLRMEHRGEVWVASGDYKLERDGTCAPF 122 +I L L YGE+I+H+GV +SLHPAGHVLGSAQ+R+EH G VWVASGDYK E DGTCAPF Sbjct: 69 DIALQTLPYGEAISHHGVRISLHPAGHVLGSAQVRLEHGGRVWVASGDYKTEPDGTCAPF 128 Query: 123 ESVRCDTFITESTFGMPIYRWQPQAEIFDDINAWWRRNAAEGRTSVLFCYAFGKAQRILH 182 E V CDTFITESTFG+PIYRW QA +F +I+AWWR NA GR SVLFCYAFGKAQRILH Sbjct: 129 EPVPCDTFITESTFGLPIYRWPTQAALFAEIDAWWRANAEAGRASVLFCYAFGKAQRILH 188 Query: 183 GLDPTIGSIVCHGAVTPLNALYREAGVALPPTLAVGDVE-DKAVLRQALVLAPPS----- 236 G+D +IG IV HGAV PLNA+YR AGVALP TL V D D A+L++ALVLAPPS Sbjct: 189 GVDASIGPIVVHGAVEPLNAVYRAAGVALPQTLRVTDAGVDAALLKRALVLAPPSAQGTP 248 Query: 237 -----------------------------------------------XASGAARIIVTHG 249 +GA R+ VTHG Sbjct: 249 WMRRFGHHADAFASGWMQLRGTRRRRGVDRGFVMSDHADWPGLQQAIAGTGAERVFVTHG 308 Query: 250 QIPIMVRWLQQNGLDAGAFDTEYGGEEEVEN 280 + +MVRWL +NGL+A F TEYG E++ + Sbjct: 309 SVAVMVRWLSENGLEAQGFRTEYGDEDDEQE 339