RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780630|ref|YP_003065043.1| ribonuclease PH [Candidatus
Liberibacter asiaticus str. psy62]
(242 letters)
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 394 bits (1016), Expect = e-111
Identities = 134/239 (56%), Positives = 175/239 (73%), Gaps = 2/239 (0%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
MR GR +Q+R +++TR +K+AEGS LV+FGDT +L TA++EE VP +++ GW+T
Sbjct: 1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVT 60
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
AEYGMLPR+T R REA G+QGGR+QEIQR+IGR+LR+VVDL ALG R I IDCDVIQ
Sbjct: 61 AEYGMLPRATHTRNDREAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQ 120
Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
ADGGTRTA+ITGA+VAL D L + K + LK VAA+S G++ G P++DLDY
Sbjct: 121 ADGGTRTASITGAYVALADALNKLVA-RGKLK-KNPLKDQVAAVSVGIVDGEPVLDLDYE 178
Query: 181 EDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
EDS + D N VMT SG VEVQG+AE A FS++ A+L+LA+ IA+L+ LQK ++
Sbjct: 179 EDSAAETDMNVVMTGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA 237
>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH. This bacterial enzyme,
ribonuclease PH, performs the final 3'-trimming and
modification of tRNA precursors. This model is
restricted absolutely to bacteria. Related families
outside the model include proteins described as probable
exosome complex exonucleases (rRNA processing) and
polyribonucleotide nucleotidyltransferases (mRNA
degradation). The most divergent member within the
family is RNase PH from Deinococcus radiodurans.
Length = 236
Score = 343 bits (881), Expect = 3e-95
Identities = 133/238 (55%), Positives = 174/238 (73%), Gaps = 2/238 (0%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITA 61
R GR+ +Q+R +S+TR K+AEGS L++FG+T +L TA++EEKVP ++R + GWITA
Sbjct: 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITA 60
Query: 62 EYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQA 121
EYGMLPR+T R +RE+ G+Q GR+QEIQR+IGRALR+VVDL ALG R I IDCDVIQA
Sbjct: 61 EYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQA 120
Query: 122 DGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYGE 181
DGGTRTA+ITGA+VAL D + + + S ++ VAA+S G++ G P++DLDY E
Sbjct: 121 DGGTRTASITGAFVALADAISKLHK-RGILKESP-IRDFVAAVSVGIVDGEPVLDLDYEE 178
Query: 182 DSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
DS DVD N VMT SG VEVQG+AE FS+D +L+LAK I +LI+LQK +
Sbjct: 179 DSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQALG 236
>gnl|CDD|179695 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 97.8 bits (244), Expect = 3e-21
Identities = 68/244 (27%), Positives = 111/244 (45%), Gaps = 27/244 (11%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTA-TLEEKVPMWIRNTKHGWI 59
+RL GR+ +++R I + V K A+GS +++G+ ++ E P ++ +
Sbjct: 14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVL 73
Query: 60 TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
Y M P S R KR R RS EI ++I AL + L I + +V+
Sbjct: 74 RVRYNMAPFSVDER-KRPGPD-R---RSIEISKVIREALEPAIMLELFPRTVIDVFIEVL 128
Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
QAD GTR A IT A +AL D M + VA + G + G ++DL+
Sbjct: 129 QADAGTRVAGITAASLALADAGIPM-------------RDLVAGCAVGKVDGVIVLDLNK 175
Query: 180 GEDSTIDVDANF-VMTDSGHIVEVQ--GSAERATFSQDHFFAMLNLAKDRIADLIKLQKD 236
ED+ + D +M G I +Q G+ +++ F L LAK I + +LQ++
Sbjct: 176 EEDNYGEADMPVAIMPRLGEITLLQLDGN-----LTREEFLEALELAKKGIKRIYQLQRE 230
Query: 237 VISN 240
+ +
Sbjct: 231 ALKS 234
>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1. This
family contains the archaeal protein orthologous to the
eukaryotic exosome protein Rrp41. It is somewhat more
distantly related to the bacterial protein ribonuclease
PH. An exosome-like complex has been demonstrated
experimentally for the Archaea in Sulfolobus
solfataricus, so members of this family are designated
exosome complex exonuclease 1, after usage in SwissProt.
Length = 230
Score = 89.4 bits (222), Expect = 7e-19
Identities = 69/242 (28%), Positives = 108/242 (44%), Gaps = 23/242 (9%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTA-TLEEKVPMWIRNTKHGWI 59
+RL GR+ +++R I + V K A+GS V+FG T ++ E P ++ +
Sbjct: 8 VRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVL 67
Query: 60 TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
Y M P ST R KR S R EI ++I AL + L I + +V+
Sbjct: 68 RVRYHMAPFSTDER-KRPGPSRR----EIEISKVIREALEPAILLEQFPRTAIDVFIEVL 122
Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
QAD GTR A +T A +AL D M D V ++ G + G ++DL+
Sbjct: 123 QADAGTRCAGLTAASLALADAGIPMRDL-------------VVGVAVGKVDGVVVLDLNE 169
Query: 180 GEDSTIDVDANF-VMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVI 238
ED + D +M G I +Q + + D F L+LA I + ++Q++ +
Sbjct: 170 EEDMYGEADMPVAMMPKLGEITLLQLDGD---MTPDEFRQALDLAVKGIKIIYQIQREAL 226
Query: 239 SN 240
N
Sbjct: 227 KN 228
>gnl|CDD|179808 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 66.4 bits (163), Expect = 6e-12
Identities = 61/257 (23%), Positives = 107/257 (41%), Gaps = 28/257 (10%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT- 60
R+ GR+ ++ R I + V K AEGS LVK G+T +L LE P + I
Sbjct: 25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVN 84
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSAL----GSRQII- 113
AE +LP ++ G + E+ R++ R +R +DL L G + +
Sbjct: 85 AE--LLPLAS-----PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVV 137
Query: 114 -IDCDVIQADGGTRTAAITGAWVAL---------HDCLQHMEDCSNKFQLSQVLKGHVAA 163
ID V+ DG A++ A AL ++ F L +
Sbjct: 138 FIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLP--VNDKPVT 195
Query: 164 ISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLA 223
++ + Y IVD E+S +D + G+IV +Q S +F+++ +++A
Sbjct: 196 VTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGI-GSFTEEEVDKAIDIA 254
Query: 224 KDRIADLIKLQKDVISN 240
++ +L + K+ +
Sbjct: 255 LEKAKELREKLKEALGI 271
>gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family).
Length = 684
Score = 39.8 bits (94), Expect = 7e-04
Identities = 39/144 (27%), Positives = 61/144 (42%), Gaps = 35/144 (24%)
Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGW----ITAEY--- 63
R ++L T ++++ A+G+ +V++GDT +L T ++ K G +T Y
Sbjct: 5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEA-------KEGQDFFPLTVNYQEK 57
Query: 64 ----GMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSR---QIIIDC 116
G +P G KRE GR + R+I R +R L G R Q++
Sbjct: 58 FYAAGKIP---GGFFKRE---GRPSEKETLTSRLIDRPIRP---LFPKGFRNEVQVV--A 106
Query: 117 DVIQADGGT--RTAAITGAWVALH 138
V+ D AI GA AL
Sbjct: 107 TVLSYDPENDPDILAIIGASAALA 130
>gnl|CDD|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 33.9 bits (79), Expect = 0.038
Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEKVP 48
R ++L T ++++ A G+ LV++GDT +L T ++
Sbjct: 14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPK 51
>gnl|CDD|180079 PRK05434, PRK05434, phosphoglyceromutase; Provisional.
Length = 507
Score = 27.0 bits (61), Expect = 4.6
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 213 QDHFFAMLNLAKDR 226
DH FA+L LAK+
Sbjct: 127 IDHLFALLELAKEE 140
>gnl|CDD|152907 pfam12473, DUF3694, Kinesin protein. This domain family is found
in eukaryotes, and is typically between 131 and 151
amino acids in length. The family is found in
association with pfam00225, pfam00498. There is a single
completely conserved residue W that may be functionally
important.
Length = 145
Score = 26.6 bits (59), Expect = 6.0
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 95 GRALRSVVDLSALGSRQIIIDCDVIQADGGTRTAAITGAW-VALHDCLQ 142
GR L + L S +++ DV GT + I W +LH+ L
Sbjct: 53 GRLLSDMHLLDPDLSLKLLSGQDVDDNADGTSSVVIEAQWDSSLHNSLL 101
>gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 26.2 bits (59), Expect = 7.3
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 156 VLKGHVAAISCGMLCGYPIVDL 177
V KG A+ G+L GYP+VD+
Sbjct: 521 VEKGVREALEKGVLAGYPVVDV 542
>gnl|CDD|172834 PRK14358, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 481
Score = 26.5 bits (58), Expect = 7.4
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 29 LVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPRSTG-NRVKREA 78
LV +GDT LL TL V + +T G LP +TG R+ R A
Sbjct: 103 LVLYGDTPLLRPDTLRALVAD--HRAQGSAMTILTGELPDATGYGRIVRGA 151
>gnl|CDD|179718 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E;
Validated.
Length = 630
Score = 25.9 bits (58), Expect = 8.8
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 51 IRNTKHGWITAEY-GMLPRSTGNRVKREAVSGRQ-------GGRSQEI 90
I + + A GML RSTG +VKR + RQ GG EI
Sbjct: 194 IHSPEQAKEVALKIGMLLRSTG-KVKRGLGTIRQDVNVSIAGGARVEI 240
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
0.321 0.134 0.393
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,800,128
Number of extensions: 231060
Number of successful extensions: 486
Number of sequences better than 10.0: 1
Number of HSP's gapped: 478
Number of HSP's successfully gapped: 16
Length of query: 242
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,028,145
Effective search space: 608249895
Effective search space used: 608249895
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 (21.9 bits)
S2: 56 (25.3 bits)