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)