RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780636|ref|YP_003065049.1| ribonuclease D [Candidatus Liberibacter asiaticus str. psy62] (207 letters) >gnl|CDD|128750 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes. Length = 172 Score = 112 bits (283), Expect = 6e-26 Identities = 56/152 (36%), Positives = 81/152 (53%), Gaps = 1/152 (0%) Query: 20 VDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKREKIF 79 +A+DTET GL +L ++Q+S II A + L +L DE K+ Sbjct: 21 GGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVG 80 Query: 80 HYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLKDNLKELLGINISKAQQSSD 139 H +FD+ VL FG+ + +F T +A+ L ++HGL LKE LG+ + K +Q SD Sbjct: 81 HNAKFDLHVL-ARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSD 139 Query: 140 WSADDLSDEQLQYAASDVVHLHALRLQFTEKL 171 W A LS+EQLQYAA D L L + ++L Sbjct: 140 WGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 >gnl|CDD|130455 TIGR01388, rnd, ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. Length = 367 Score = 92.5 bits (230), Expect = 7e-20 Identities = 55/194 (28%), Positives = 92/194 (47%), Gaps = 14/194 (7%) Query: 7 HEGDIPAEC-AARYVDAIAVDTETLGLMPRRDR-----LCIVQLSPGDGTVDIIRIAAGQ 60 + ++ C A R +A+DTE + R+R L ++Q++ G+ I + Sbjct: 4 TDDELATVCEAVRTFPFVALDTEFV-----RERTFWPQLGLIQVADGEQLALIDPLVIID 58 Query: 61 KNAPNLVGMLVDEKREKIFHYGRFDIAVLFYTFGVRVRPVFCTKIASRLTRTYTNQHGLK 120 + L +L DE K+ H D+ V FG +P+F T+IA+ + G Sbjct: 59 WSP--LKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFC-GFGMSMGYA 115 Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 ++E+LG+ + K++ +DW A L+D QL+YAA+DV +L L + E+L+ GR Sbjct: 116 KLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWL 175 Query: 181 TSCCNFLMDRAELD 194 C L DR Sbjct: 176 EEECTLLTDRRTYV 189 >gnl|CDD|182762 PRK10829, PRK10829, ribonuclease D; Provisional. Length = 373 Score = 57.3 bits (139), Expect = 3e-09 Identities = 50/176 (28%), Positives = 82/176 (46%), Gaps = 5/176 (2%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNAPNLVGMLVDEKR 75 AAR AIA+DTE + +L ++QL G+ + +I +P +L D + Sbjct: 18 AARAFPAIALDTEFVRTRTYYPQLGLIQLYDGE-QLSLIDPLGITDWSP-FKALLRDPQV 75 Query: 76 EKIFHYGRFDIAVLFYTFGVRVRPVFCTKI-ASRLTRTYTNQHGLKDNLKELLGINISKA 134 K H G D+ V FG +P+ T+I A+ R + G ++E G+ + K+ Sbjct: 76 TKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLS--CGFASMVEEYTGVTLDKS 133 Query: 135 QQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLATSCCNFLMDR 190 + +DW A LS+ Q +YAA+DV +L + + + + G A C L R Sbjct: 134 ESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQR 189 >gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional. Length = 880 Score = 53.2 bits (129), Expect = 5e-08 Identities = 37/161 (22%), Positives = 62/161 (38%), Gaps = 7/161 (4%) Query: 16 AARYVDAIAVDTETLGLMPRRDRLCIVQLSPGDGTVDIIRIAAGQKNA-PNLVGMLVDEK 74 + A DTET L P + L + + G I + + L +L D Sbjct: 311 KLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370 Query: 75 REKIFHYGRFDIAVLFYTFGVRVRPV-FCTKIASRLTRTYTNQHGLKDNLKELLGINISK 133 +K+ ++D+ VL +G+ +R + F T +AS L +HGL + LG Sbjct: 371 IKKVGQNLKYDLHVL-ARYGIELRGIAFDTMLASYLLDP-GRRHGLDSLAERYLGHKTIS 428 Query: 134 AQQS--SDWSADDLSDEQL-QYAASDVVHLHALRLQFTEKL 171 ++ + + E+ +YAA D L KL Sbjct: 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKL 469 >gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional. Length = 553 Score = 52.3 bits (126), Expect = 1e-07 Identities = 26/86 (30%), Positives = 35/86 (40%), Gaps = 3/86 (3%) Query: 91 YTFGVRVRPVFCTKIASRLTRTYTN--QHGLKDNLKELLGINISKAQQSSDWSADDLSDE 148 GVRV +AS+L L LG + K Q+S S D +E Sbjct: 63 LAAGVRVERCHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEE 121 Query: 149 QLQYAASDVVHLHALRLQFTEKLQRL 174 QL YAA+D L L ++L R+ Sbjct: 122 QLLYAAADADVLLELYAVLADQLNRI 147 >gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated. Length = 328 Score = 30.4 bits (69), Expect = 0.29 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%) Query: 121 DNLKELLGINISKAQQSSDWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQRLGRSDLA 180 D +K+LL S +Q + W L L D H LR Q T+ + LG +D+ Sbjct: 217 DGVKKLLKQQQSASQLAESWLKVPLL--LLFDWFCDWAHD-ILRYQLTQDEEGLGLADMR 273 Query: 181 TS 182 Sbjct: 274 KV 275 >gnl|CDD|179264 PRK01254, PRK01254, hypothetical protein; Provisional. Length = 707 Score = 28.9 bits (65), Expect = 1.1 Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%) Query: 186 FL-MDRAELDLLGWENVDI 203 FL M R E+D LGW++ DI Sbjct: 24 FLPMSREEMDQLGWDSCDI 42 >gnl|CDD|149520 pfam08497, Radical_SAM_N, Radical SAM N-terminal. This domain tends to occur to the N-terminus of the pfam04055 domain in hypothetical bacterial proteins. Length = 298 Score = 28.2 bits (64), Expect = 1.7 Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 1/19 (5%) Query: 186 FL-MDRAELDLLGWENVDI 203 FL R E+ GW+ +D+ Sbjct: 1 FLPTSREEMKARGWDQLDV 19 >gnl|CDD|149870 pfam08936, CsoSCA, Carboxysome Shell Carbonic Anhydrase. Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localized in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain. Length = 459 Score = 27.6 bits (62), Expect = 2.3 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 13/59 (22%) Query: 4 IRVHEGDIPAE----CAARYVDAIAVDTETLGLMPRRDRLCIVQL------SPGDGTVD 52 IRVH +P R+VD + ETLGL + R I + + G G D Sbjct: 251 IRVH---VPDADGEVDLDRWVDTADLYRETLGLSAEQARAAIAEAVAADGWAQGPGAPD 306 >gnl|CDD|162979 TIGR02701, shell_carb_anhy, carboxysome shell carbonic anhydrase. This model describes a carboxysome shell protein that proves to be a novel class, designated epsilon, of carbonic anhydrase. It tends to be encoded near genes for RuBisCo and for other carboxysome shell proteins. Length = 450 Score = 26.3 bits (58), Expect = 5.3 Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 7/44 (15%) Query: 4 IRVHEGDIPAE----CAARYVDAIAVDTETLGLMPRRDRLCIVQ 43 IRVH IP RYVD + ETLGL R I + Sbjct: 252 IRVH---IPDADGFVNLYRYVDNTVLYAETLGLTADEARQHIAE 292 >gnl|CDD|181529 PRK08662, PRK08662, nicotinate phosphoribosyltransferase; Reviewed. Length = 343 Score = 26.4 bits (59), Expect = 5.6 Identities = 8/15 (53%), Positives = 11/15 (73%) Query: 190 RAELDLLGWENVDIF 204 R LD+ G+E+V IF Sbjct: 251 RWTLDIRGYEHVKIF 265 >gnl|CDD|178146 PLN02531, PLN02531, GTP cyclohydrolase I. Length = 469 Score = 26.3 bits (58), Expect = 6.1 Identities = 8/17 (47%), Positives = 11/17 (64%) Query: 157 VVHLHALRLQFTEKLQR 173 +VH + RLQ E+L R Sbjct: 385 IVHFYGFRLQVQERLTR 401 >gnl|CDD|181680 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated. Length = 294 Score = 26.1 bits (58), Expect = 7.2 Identities = 9/16 (56%), Positives = 12/16 (75%) Query: 22 AIAVDTETLGLMPRRD 37 + +DTET GL PR+D Sbjct: 39 GVILDTETTGLDPRKD 54 >gnl|CDD|181671 PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated. Length = 202 Score = 25.6 bits (57), Expect = 8.4 Identities = 9/17 (52%), Positives = 12/17 (70%) Query: 23 IAVDTETLGLMPRRDRL 39 +A+D ET GL PRR + Sbjct: 32 VALDCETTGLDPRRAEI 48 >gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated. Length = 319 Score = 25.7 bits (56), Expect = 8.8 Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 27/98 (27%) Query: 122 NLKELLGINISKAQQSSDWSADDLSDEQLQYAA-----------SDVVHLHALRLQF--- 167 +L+++ + W+ D +D++L++AA +D LH L F Sbjct: 223 DLEQIASGRAGAVDVAQRWTNDGQADQRLRHAADLALAQASAGLTDPSRLHKLATWFDAA 282 Query: 168 --TEKLQRLG-RSDLATSCCNFLMDRAELDLLGWENVD 202 T L R R+DLA EL LL W + Sbjct: 283 NRTRDLLRTTVRADLAV---------TEL-LLAWREGE 310 >gnl|CDD|179566 PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated. Length = 380 Score = 25.6 bits (56), Expect = 8.9 Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 7/35 (20%) Query: 169 EKLQRLG-RSDLATSCCNFLMDRAEL---DLLGWE 199 KL++LG R D SCC D EL D+ G E Sbjct: 195 TKLEKLGLRMD---SCCEITFDDVELDEKDMFGRE 226 >gnl|CDD|147901 pfam05992, SbmA_BacA, SbmA/BacA-like family. The Rhizobium meliloti bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of BacA, SbmA, is implicated in the uptake of microcins and bleomycin. This family is likely to be a subfamily of the ABC transporter family. Length = 315 Score = 25.8 bits (57), Expect = 9.3 Identities = 8/13 (61%), Positives = 10/13 (76%) Query: 79 FHYGRFDIAVLFY 91 FHY F+IA +FY Sbjct: 235 FHYLYFNIARIFY 247 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.137 0.408 Gapped Lambda K H 0.267 0.0645 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,427,955 Number of extensions: 215210 Number of successful extensions: 407 Number of sequences better than 10.0: 1 Number of HSP's gapped: 399 Number of HSP's successfully gapped: 25 Length of query: 207 Length of database: 5,994,473 Length adjustment: 89 Effective length of query: 118 Effective length of database: 4,071,361 Effective search space: 480420598 Effective search space used: 480420598 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 55 (25.1 bits)