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)