RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed. Length = 235 Score = 397 bits (1021), Expect = e-111 Identities = 134/227 (59%), Positives = 171/227 (75%) Query: 1 MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLF 60 ++A S LE+R G+ FAN+ LE+ALTHSS S Q +YERLEFLGDR+LGL ++ +LF Sbjct: 7 LAAATASILEERTGHRFANKERLERALTHSSARASKQGNYERLEFLGDRVLGLCVAEMLF 66 Query: 61 NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVE 120 F A EGELSVR N LV+AETC+ +A E+ L IR SD++K + +++ADVVE Sbjct: 67 EAFPDASEGELSVRLNQLVNAETCAAIADEIGLHDLIRTGSDVKKLTGKRLLNVRADVVE 126 Query: 121 SLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFR 180 +LIAA+YLDGG+E A F+ +YW++RAL++ RRDAKTELQEWAHA+FGVTP Y+V R Sbjct: 127 ALIAAIYLDGGLEAARPFIQRYWQKRALETDAARRDAKTELQEWAHAQFGVTPVYRVDSR 186 Query: 181 SGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT 227 SGPDHDPRFTV VE+ G AP G SKRAAEQVAA ++L+REG+W Sbjct: 187 SGPDHDPRFTVEVEVKGFAPETGEGRSKRAAEQVAAEKMLEREGVWK 233 >gnl|CDD|162755 TIGR02191, RNaseIII, ribonuclease III, bacterial. This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. Length = 220 Score = 251 bits (643), Expect = 1e-67 Identities = 98/220 (44%), Positives = 132/220 (60%), Gaps = 5/220 (2%) Query: 9 LEKRIGYAFANRSLLEKALTHSSIS---HSYQESYERLEFLGDRILGLLISTLLFNHFDS 65 LEKR+GY F N+ LLE+ALTHSS + H ++ ERLEFLGD +LGL+++ LF +F Sbjct: 1 LEKRLGYKFKNKELLEQALTHSSYANEHHKGVKNNERLEFLGDAVLGLVVAEYLFKNFPD 60 Query: 66 AKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA 125 EGELS +LVS E+ ++VAREL L F+ + K SI AD E+LI A Sbjct: 61 LSEGELSKLRAALVSEESLAEVARELGLGKFLLLGKGEEKSGGRRRESILADAFEALIGA 120 Query: 126 LYLDGGIEVAGTFVDKYWKQR--ALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGP 183 +YLD G+E A F+ K R A++ + +D KT LQEWA A+ PEY++ GP Sbjct: 121 IYLDSGLEAARKFILKLLIPRIDAIEKEETLKDYKTALQEWAQARGKPLPEYRLIKEEGP 180 Query: 184 DHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE 223 DHD FTV V ++G +G SK+ AEQ AA L++ Sbjct: 181 DHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEKL 220 >gnl|CDD|178863 PRK00102, rnc, ribonuclease III; Reviewed. Length = 229 Score = 223 bits (572), Expect = 2e-59 Identities = 84/228 (36%), Positives = 124/228 (54%), Gaps = 18/228 (7%) Query: 6 YSTLEKRIGYAFANRSLLEKALTHSSISHSYQ--ESYERLEFLGDRILGLLISTLLFNHF 63 L+K++GY F + LL +ALTH S ++ + + ERLEFLGD +L L++S LF F Sbjct: 5 LEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLELVVSEYLFKRF 64 Query: 64 DSAKEGELSVRFNSLVSAETCSQVARELDLASFIR------VSSDLRKDVCSFMTSIQAD 117 EG+LS +LV E+ +++AREL L ++ S R+ SI AD Sbjct: 65 PDLDEGDLSKLRAALVREESLAEIARELGLGEYLLLGKGEEKSGGRRRP------SILAD 118 Query: 118 VVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR---RDAKTELQEWAHAKFGVTPE 174 E+LI A+YLD G+E A F+ + ++ R ++ +D KT LQE + PE Sbjct: 119 AFEALIGAIYLDQGLEAARKFILRLFEPR-IEEIDLGDLVKDYKTRLQELLQGRGLPLPE 177 Query: 175 YKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKR 222 Y++ GP HD FTV V ++G +G SK+ AEQ AA + LK+ Sbjct: 178 YELVKEEGPAHDKEFTVEVTVNGKELGEGTGSSKKEAEQAAAKQALKK 225 >gnl|CDD|128808 smart00535, RIBOc, Ribonuclease III family. Length = 129 Score = 130 bits (330), Expect = 2e-31 Identities = 53/127 (41%), Positives = 75/127 (59%), Gaps = 1/127 (0%) Query: 21 SLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVS 80 SLL +ALTH+S S+ E ERLEFLGD +L L+++ L+ + EG+LS ++LVS Sbjct: 1 SLLLRALTHASYSNE-HEHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVS 59 Query: 81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVD 140 ET +++A++L L FIR+ SI ADV E+LI A+YLD G+E A F+ Sbjct: 60 NETLARLAKKLGLGEFIRLGRGEAISGGRDKPSILADVFEALIGAIYLDSGLEAAREFIR 119 Query: 141 KYWKQRA 147 R Sbjct: 120 DLLGPRL 126 >gnl|CDD|183478 PRK12372, PRK12372, ribonuclease III; Reviewed. Length = 413 Score = 108 bits (270), Expect = 1e-24 Identities = 84/229 (36%), Positives = 116/229 (50%), Gaps = 30/229 (13%) Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66 S LE R+ Y F N LL +ALTH S S ++ E RLEFLGD +L ++ LLF F Sbjct: 4 SQLESRLRYEFRNAELLRQALTHRSHSATHNE---RLEFLGDSVLNCAVAALLFQRFGKL 60 Query: 67 KEGELS-VRFNSLVSAETCSQVARELDLASFIRV------SSDLRKDVCSFMTSIQADVV 119 EG+LS VR N LV ++ ++A+ L+++ +R+ S R+ SI AD Sbjct: 61 DEGDLSRVRAN-LVKQQSLYEIAQALNISEGLRLGEGELRSGGFRR------PSILADAF 113 Query: 120 ESLIAALYLDGGIEVAGTFVDKYW-------KQRALKSGKFRRDAKTELQEWAHAKFGVT 172 E++I A++LDGG E A + + + R L GK DAKT LQE+ Sbjct: 114 EAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDPRTL--GK---DAKTLLQEYLQGHKIAL 168 Query: 173 PEYKVTFRSGPDHDPRFTVVVEISGL-APAQGMDCSKRAAEQVAAAEVL 220 P Y V G H+ +F V + L G S+RAAEQ AA + L Sbjct: 169 PTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKKAL 217 >gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional. Length = 467 Score = 106 bits (266), Expect = 4e-24 Identities = 75/217 (34%), Positives = 110/217 (50%), Gaps = 6/217 (2%) Query: 7 STLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSA 66 S LE R+ Y F N LL +ALTH S S ++ E RLEFLGD +L ++ LLF F Sbjct: 4 SQLESRLRYEFRNAELLRQALTHRSHSATHNE---RLEFLGDSVLNCAVAALLFQRFGKL 60 Query: 67 KEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAAL 126 EG+LS +LV ++ ++A+ L+++ +R+ + SI AD E++I A+ Sbjct: 61 DEGDLSRVRANLVKQQSLYEIAQALNISDGLRLGEGELRSGGFRRPSILADAFEAIIGAV 120 Query: 127 YLDGGIEVAGTFVDKYWKQ--RALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD 184 +LDGG E A + + + + +DAKT LQE+ P Y V G Sbjct: 121 FLDGGFEAAQGVIKRLYVPILDHIDPRTLGKDAKTLLQEYLQGHKIALPTYTVVATHGAA 180 Query: 185 HDPRFTVVVEISGL-APAQGMDCSKRAAEQVAAAEVL 220 H+ +F V + L G S+RAAEQ AA + L Sbjct: 181 HNQQFEVECTVPKLDIKVSGSGASRRAAEQAAAKKAL 217 >gnl|CDD|128652 smart00358, DSRM, Double-stranded RNA binding motif. Length = 67 Score = 70.8 bits (174), Expect = 3e-13 Identities = 29/65 (44%), Positives = 39/65 (60%), Gaps = 1/65 (1%) Query: 157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAA 216 K+ LQE A K G+ PEY++ GPDH PRFTV V++ G +G SK+ A+Q AA Sbjct: 1 PKSLLQELA-QKRGLPPEYELVKEEGPDHAPRFTVTVKVGGEYTGEGEGSSKKEAKQRAA 59 Query: 217 AEVLK 221 L+ Sbjct: 60 EAALR 64 >gnl|CDD|177482 PHA02701, PHA02701, ORF020 dsRNA-binding PKR inhibitor; Provisional. Length = 183 Score = 35.3 bits (81), Expect = 0.012 Identities = 18/47 (38%), Positives = 23/47 (48%) Query: 174 EYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVL 220 E+ T G DH P FT + +SG A CSK+ A A A+ L Sbjct: 126 EFCETRSGGHDHCPLFTCTIVVSGKVVATASGCSKKLARHAACADAL 172 >gnl|CDD|177529 PHA03103, PHA03103, double-strand RNA-binding protein; Provisional. Length = 183 Score = 34.7 bits (80), Expect = 0.022 Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 4/41 (9%) Query: 180 RSGPDHDPRFTVVVEISGLA--PAQGMDCSKRAAEQVAAAE 218 SGP H P FT V ISG+ PA G +K+ A+ AA Sbjct: 132 SSGPSHSPTFTASVIISGIKFKPAIGS--TKKEAKNNAAKL 170 >gnl|CDD|131363 TIGR02310, HpaB-2, 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Shigella, Photorhabdus and Pasteurella. The family modelled by this alignment is narrowly limited to gammaproteobacteria to exclude other aromatic hydroxylases involved in various secondary metabolic pathways. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241). Length = 519 Score = 29.5 bits (66), Expect = 0.66 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%) Query: 136 GTFVDKYWK-QRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRF 189 G + K+++ R+ + +RDA E ++ G TP+YK F S +P F Sbjct: 76 GGYTHKFFRYARSADELRQQRDAIAEWSRLSYGWMGRTPDYKAAFGSALGANPGF 130 >gnl|CDD|150182 pfam09423, PhoD, PhoD-like phosphatase. Length = 450 Score = 28.7 bits (65), Expect = 1.3 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 2/25 (8%) Query: 178 TFRSGPDHDPRFTVVVEISGLAPAQ 202 T + P+ D TV VE++GL P + Sbjct: 53 TATATPERD--HTVKVEVTGLPPGR 75 >gnl|CDD|180287 PRK05849, PRK05849, hypothetical protein; Provisional. Length = 783 Score = 26.1 bits (58), Expect = 8.3 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 8/69 (11%) Query: 48 DRILGLL-----ISTLLFNHFDSAKEGELSVRF-NSLVSAETCSQVARELDLASFIRVSS 101 D+I LL TL F A+ ++ + SLV SQ + L S VS Sbjct: 435 DKIYWLLEDCKRYGTLPFAG--IARAAFVATQLLKSLVEIGALSQEELDAFLNSLNTVSK 492 Query: 102 DLRKDVCSF 110 +L KD+ S Sbjct: 493 ELSKDLNSL 501 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 0.319 0.132 0.377 Gapped Lambda K H 0.267 0.0699 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,624,266 Number of extensions: 224682 Number of successful extensions: 426 Number of sequences better than 10.0: 1 Number of HSP's gapped: 410 Number of HSP's successfully gapped: 21 Length of query: 227 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 137 Effective length of database: 4,049,753 Effective search space: 554816161 Effective search space used: 554816161 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 (25.0 bits)