RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780630|ref|YP_003065043.1| ribonuclease PH [Candidatus
Liberibacter asiaticus str. psy62]
(242 letters)
>gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 247 bits (632), Expect = 2e-66
Identities = 114/240 (47%), Positives = 156/240 (65%), Gaps = 18/240 (7%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTAT-LEEKVPMWIRNTKHGWI 59
MR GR+ +++R I +TR V K+AEGS L++FG+T ++ T + E VP ++R T GW+
Sbjct: 8 MRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWL 67
Query: 60 TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119
TAEYGMLPRST R KREA GR ++EI R+IGRALR+V+DL L I IDCDV+
Sbjct: 68 TAEYGMLPRSTDERKKREADRGR----TKEISRLIGRALRAVIDLELLPESTIDIDCDVL 123
Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179
QADGGTRTA+ITGA +AL D + D VAAIS G++ G ++DLDY
Sbjct: 124 QADGGTRTASITGASLALADAGIPLRDL-------------VAAISVGIVDGVIVLDLDY 170
Query: 180 GEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239
EDS + D N VMT +G +VE+QG AE F++D +L+LA +L +LQ++ ++
Sbjct: 171 EEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230
>gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 128
Score = 120 bits (304), Expect = 3e-28
Identities = 47/130 (36%), Positives = 63/130 (48%), Gaps = 6/130 (4%)
Query: 10 QMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPRS 69
++R I + V A+GS LV+ GDT +L T T + P R+ G +T EY P +
Sbjct: 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPNE-RDFFPGELTVEYEEKPFA 59
Query: 70 TGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADGGTRTAA 129
+G R GR R E+ R+I RALR L +I ID V+ DG AA
Sbjct: 60 SGERP-----EGRPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGSLLDAA 114
Query: 130 ITGAWVALHD 139
I A +AL D
Sbjct: 115 INAASLALAD 124
>gnl|CDD|36286 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp41 and related exoribonucleases [Translation,
ribosomal structure and biogenesis].
Length = 245
Score = 84.6 bits (209), Expect = 2e-17
Identities = 58/242 (23%), Positives = 93/242 (38%), Gaps = 26/242 (10%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTT-ATLEEKVPMWIRNTKHGWIT 60
R GR+ N++R I V A+GS ++ G+T +L E R +
Sbjct: 14 RTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLN 73
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120
E STG+R KR + R +E+ M+ +A V+ L QI I V++
Sbjct: 74 CEVSSAQFSTGDRKKRP----KGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLE 129
Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180
DG AAI A +AL D M D + A + G+ G P++DL
Sbjct: 130 DDGSNLAAAINAATLALADAGIPMYDL-------------ITACTAGLADGTPLLDLTSL 176
Query: 181 EDSTIDVD---ANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDV 237
E+S A + ++++ DH +L LA + + + V
Sbjct: 177 EESARAPGLTVAALPNREEIALLQLDER-----LHCDHLETVLELAIAGCKRVYERLRLV 231
Query: 238 IS 239
+
Sbjct: 232 LR 233
>gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 69.2 bits (169), Expect = 1e-12
Identities = 49/257 (19%), Positives = 93/257 (36%), Gaps = 26/257 (10%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKH-GWIT 60
R+ GR ++ R + + V A GS LVK G+T ++ E P +T + G +
Sbjct: 24 RIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPF--PDTPNEGVLV 81
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSV--VDLSALGSRQ------I 112
+ P ++ + E G + E+ R++ R LR +DL L + +
Sbjct: 82 VNVELSPLASPS---FEP--GPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVV 136
Query: 113 IIDCDVIQADGGTRTAAITGAWVAL---------HDCLQHMEDCSNKFQLSQVLKGHVAA 163
+D V+ DG AA A AL + + + + +
Sbjct: 137 FVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPIS 196
Query: 164 ISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLA 223
++ + +VD E+ D + + G IV +Q + ++ L A
Sbjct: 197 VTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQ-KVGGGSITESDLEKALKTA 255
Query: 224 KDRIADLIKLQKDVISN 240
+ L + K+ +
Sbjct: 256 LSKAEKLREALKEALKE 272
>gnl|CDD|146389 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2. This
family includes 3'-5' exoribonucleases. Ribonuclease PH
contains a single copy of this domain, and removes
nucleotide residues following the -CCA terminus of tRNA.
Polyribonucleotide nucleotidyltransferase (PNPase)
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction. The
exosome is a 3'-5' exoribonuclease complex that is
required for 3' processing of the 5.8S rRNA. Three of
its five protein components contain a copy of this
domain. A hypothetical protein from S. pombe appears to
belong to an uncharacterized subfamily. This subfamily
is found in both eukaryotes and archaebacteria.
Length = 67
Score = 54.5 bits (132), Expect = 2e-08
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 159 GHVAAISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFA 218
G VAA++ G + G ++D E+S D D V+ +G IV + +++
Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGDIVALM-KEGGGGLTEEELLE 59
Query: 219 MLNLAKDR 226
L LA
Sbjct: 60 ALELAHKG 67
>gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide
nucleotidyltransferase [General function prediction
only].
Length = 760
Score = 44.2 bits (104), Expect = 3e-05
Identities = 58/238 (24%), Positives = 100/238 (42%), Gaps = 42/238 (17%)
Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEK------VPMWIRNTKHGWITAEYG 64
REI T +++++A GS +V+ G+T ++TT L +K +P+ + + A G
Sbjct: 56 REILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQFLPLVV---DYQEKFAAVG 112
Query: 65 MLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADG- 123
+P GN ++RE GR + R+I R +R + QI+ C+V+ +DG
Sbjct: 113 RIP---GNFMRRE---GRTKDKEILTGRLIDRPIRPLFPKGFYHETQIL--CNVLSSDGV 164
Query: 124 -GTRTAAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYPIVDLDYGE 181
AI A AL LS V G + A+ G++ G +V+ E
Sbjct: 165 HDPDVLAINAASAAL--------------SLSDVPWNGPIGAVRIGLIDGEFVVNPTRKE 210
Query: 182 DSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDR----IADLIKLQK 235
S+ ++ T S V ++GS+ Q + + I + +L K
Sbjct: 211 MSSSQLNLVVAGTKS-QTVMLEGSSN--NILQQDLLHAIKVGVKEAQQIIQGIERLAK 265
Score = 43.1 bits (101), Expect = 7e-05
Identities = 43/186 (23%), Positives = 74/186 (39%), Gaps = 27/186 (14%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLE-----EKVPMWIRNTKH 56
R GR +++R IS + K GS L + G T +L T TL+ +K+ I
Sbjct: 359 RCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNG 418
Query: 57 GWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116
Y P +T K ++ R+ G + +AL V L I +
Sbjct: 419 INFMLHYEFPPYATNEVGKIGGLNRRELGHGA----LAEKALLPV--LPEDFPFTIRVTS 472
Query: 117 DVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVD 176
+V++++G + A++ G +AL D + HVA ++ G++ D
Sbjct: 473 EVLESNGSSSMASVCGGSLALMDA-------------GVPVSAHVAGVAIGLVTK---TD 516
Query: 177 LDYGED 182
+ GE
Sbjct: 517 PEKGEI 522
>gnl|CDD|36827 KOG1614, KOG1614, KOG1614, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp45 [Translation, ribosomal structure and
biogenesis].
Length = 291
Score = 43.4 bits (102), Expect = 5e-05
Identities = 52/262 (19%), Positives = 90/262 (34%), Gaps = 34/262 (12%)
Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGW-IT 60
R GR + R++ + GS LV G+T ++ T + P R + + I
Sbjct: 23 RFDGRSLEEFRDLEIEFGKEY---GSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIF 79
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSALGSR------QI 112
E + + GR+G E+ R+I +ALR +D +L R I
Sbjct: 80 TELSPMASPSFE-------PGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLI 132
Query: 113 IIDCDVIQADGGTRTAAITGAWVALH-----DCLQHMEDCSNKFQLSQV---LKGHVAAI 164
ID ++ DG AA AL D E+ + L H I
Sbjct: 133 RIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPI 192
Query: 165 SCGMLC-----GYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAM 219
C ++D E++ +D M + + +Q + +
Sbjct: 193 -CFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQ-KSGGEILDESVIERC 250
Query: 220 LNLAKDRIADLIKLQKDVISNE 241
LAKDR ++ + + + +
Sbjct: 251 YKLAKDRAVEVTGIILEALEED 272
>gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 38.2 bits (89), Expect = 0.002
Identities = 52/243 (21%), Positives = 89/243 (36%), Gaps = 54/243 (22%)
Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEK------VPMWIRNTKHGWITAEY- 63
R ++L T ++++ A G+ LV++GDT +L T + P+ T Y
Sbjct: 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPL----------TVNYE 63
Query: 64 ------GMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQ-IIIDC 116
G +P G KRE GR + R+I R +R L G R + I
Sbjct: 64 EKTYAAGKIP---GGFFKRE---GRPSEKEILTSRLIDRPIRP---LFPKGFRNEVQIVN 114
Query: 117 DVIQADGGT--RTAAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYP 173
V+ D A+ GA AL LS + G + A+ G + G
Sbjct: 115 TVLSVDPENDPDILAMVGASAALS--------------LSGIPFLGPIGAVRVGYIDGIF 160
Query: 174 IVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKL 233
+++ E +D V + V+ A+ ++ + + I +I
Sbjct: 161 VLNPTLEELEESKLD-LVVAGTKDAVNMVESEAD--ELDEEVMLEAVEFGHEAIQSVINA 217
Query: 234 QKD 236
Q++
Sbjct: 218 QEE 220
>gnl|CDD|36826 KOG1613, KOG1613, KOG1613, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp43 [Translation, ribosomal structure and
biogenesis].
Length = 298
Score = 33.8 bits (77), Expect = 0.042
Identities = 32/153 (20%), Positives = 58/153 (37%), Gaps = 18/153 (11%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60
+R GR+ + R+ ++ A GS L+K G T ++ E P G I
Sbjct: 36 IRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPS-TDAPDEGDIV 94
Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSAL----GSRQIII 114
Y + P + +R + G +Q I + + + ++ AL G ++
Sbjct: 95 PNYALPPLCS-SRFR----PGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVL 149
Query: 115 DCDVI--QADGGTRTAAITGAWVALHDCLQHME 145
D+I DG W AL L++++
Sbjct: 150 YADIICLDYDG----PVFDACWNALMAALKNVK 178
>gnl|CDD|58274 cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain IV
of the bacterial translational elongation factor (EF)
EF-G. Included in this group is a domain of
mitochondrial Elongation factor G1 (mtEFG1) proteins
homologous to domain IV of EF-G. Eukaryotic cells harbor
2 protein synthesis systems: one localized in the
cytoplasm, the other in the mitochondria. Most factors
regulating mitochondrial protein synthesis are encoded
by nuclear genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. During the process
of peptide synthesis and tRNA site changes, the ribosome
is moved along the mRNA a distance equal to one codon
with the addition of each amino acid. In bacteria this
translocation step is catalyzed by EF-G_GTP, which is
hydrolyzed to provide the required energy. Thus, this
action releases the uncharged tRNA from the P site and
transfers the newly formed peptidyl-tRNA from the A site
to the P site. Eukaryotic mtEFG1 proteins show
significant homology to bacterial EF-Gs. Mutants in
yeast mtEFG1 have impaired mitochondrial protein
synthesis, respiratory defects and a tendency to lose
mitochondrial DNA. There are two forms of mtEFG present
in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are
not present in this group..
Length = 116
Score = 29.2 bits (66), Expect = 1.00
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 156 VLKGHVAAISCGMLCGYPIVDL 177
V KG A+ G L GYP+VD+
Sbjct: 60 VEKGFREALEKGPLAGYPVVDV 81
>gnl|CDD|36825 KOG1612, KOG1612, KOG1612, Exosomal 3'-5' exoribonuclease
complex, subunit Rrp42 [Translation, ribosomal
structure and biogenesis].
Length = 288
Score = 27.3 bits (60), Expect = 3.6
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDT 35
+R GR +Q R I + V GS VK GD
Sbjct: 21 IRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDG 55
>gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 26.0 bits (57), Expect = 8.8
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 153 LSQVLKGHVAAISCGMLCGYPIVDL 177
+ V KG A+ G L GYP+VD+
Sbjct: 537 IPAVEKGFREALKSGPLAGYPVVDV 561
>gnl|CDD|146417 pfam03764, EFG_IV, Elongation factor G, domain IV. This domain is
found in elongation factor G, elongation factor 2 and
some tetracycline resistance proteins and adopts a
ribosomal protein S5 domain 2-like fold.
Length = 120
Score = 26.0 bits (58), Expect = 9.1
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 156 VLKGHVAAISCGMLCGYPIVDL 177
V KG A+ G L G P+ D+
Sbjct: 64 VEKGFQEAMKEGPLAGEPVRDV 85
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.134 0.393
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,722,257
Number of extensions: 134015
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 18
Length of query: 242
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 151
Effective length of database: 4,297,318
Effective search space: 648895018
Effective search space used: 648895018
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 (25.2 bits)