RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18119
(263 letters)
>gnl|CDD|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome. The
RRP41 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 226
Score = 356 bits (917), Expect = e-126
Identities = 132/225 (58%), Positives = 176/225 (78%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
GLR DGRR +ELR+IRCR+GVFS +DGSAY+EQGNTKVLAAVYGP RN+S +H +
Sbjct: 1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAV 60
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
+N +YSMA FSTGERK R +GDR+++E+SL +RQ A I++ ++PRSQIDI+V+VLQAD
Sbjct: 61 VNCEYSMATFSTGERKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQAD 120
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
GG AC+NAATLALIDAGIPM++YV ACSA TPL+D+++LEE+ P+LTVA LP
Sbjct: 121 GGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPLLDLNYLEESGDLPDLTVAVLP 180
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
S KV ++++ +LHLD L +VL+ A++GC I I+D +++H
Sbjct: 181 KSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHT 225
>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 219 bits (559), Expect = 1e-71
Identities = 93/230 (40%), Positives = 142/230 (61%), Gaps = 1/230 (0%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
GLR DGR+ ELR I+ +GV +DGSAY+E GN K++AAVYGPR + + +++ +
Sbjct: 13 GLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAV 72
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
+ +Y+MA FS ERK RP DR++ EIS +R+A+ AIM E+ PR+ ID+F+EVLQAD
Sbjct: 73 LRVRYNMAPFSVDERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQAD 131
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
G A + AA+LAL DAGIPMR+ V C+ ++D++ E+ G ++ VA +P
Sbjct: 132 AGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMP 191
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
G++ +++L L + L+ A KG I+ + A+K ++A
Sbjct: 192 RLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIAE 241
>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
[Transcription, Degradation of RNA].
Length = 230
Score = 206 bits (526), Expect = 1e-66
Identities = 96/223 (43%), Positives = 140/223 (62%), Gaps = 1/223 (0%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
G+R DGR+ ELR I+ GV +DGSAY+E G TK+LAAVYGPR + +++ +
Sbjct: 7 GVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAV 66
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
+ +Y MA FST ERK RP R+ EIS +R+A+ AI+ E PR+ ID+F+EVLQAD
Sbjct: 67 LRVRYHMAPFSTDERK-RPGPSRREIEISKVIREALEPAILLEQFPRTVIDVFIEVLQAD 125
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
GG CA + AA+LAL DAGIPMR+ VV + ++D+S E+ G ++ VA +P
Sbjct: 126 GGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMYGEADMPVAIMP 185
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
+G++ +++L L D + LD A++G I+ I A+K+
Sbjct: 186 KTGEITLLQLDGDLTPDEFRQALDLAVEGIKRIYEIQREALKK 228
>gnl|CDD|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome.
The RRP41 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA.
Length = 214
Score = 204 bits (521), Expect = 3e-66
Identities = 90/212 (42%), Positives = 135/212 (63%), Gaps = 1/212 (0%)
Query: 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
ELR I+ +GV +DGSAY+E GN K++AAVYGPR V + +++ +I +Y+MA F
Sbjct: 1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPF 60
Query: 80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
S ERK RP DR+ EIS +++A+ AI+ E PR+ ID+FVEVLQAD G A +NA
Sbjct: 61 SVDERK-RPGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNA 119
Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL 199
A+LAL DAGIPMR+ V AC+A ++D++ E+ G ++ +A +P G++ +++L
Sbjct: 120 ASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGEITLLQL 179
Query: 200 SQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
L D + ++ A KGC I+ + A+K
Sbjct: 180 DGDLTPDEFKQAIELAKKGCKRIYELQKEALK 211
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 202 bits (517), Expect = 3e-65
Identities = 81/224 (36%), Positives = 120/224 (53%), Gaps = 2/224 (0%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
G+R DGR+ ELR I+ GV ++GS+ IE GNTKV+ V GPR + ++ G
Sbjct: 7 GMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGW 66
Query: 70 INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
+ +Y M ST ERK R +T EIS + +A+ A I E+ P S IDI +VLQAD
Sbjct: 67 LTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQAD 126
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
GG A + A+LAL DAGIP+R+ V A S + ++D+ + E++ ++ V
Sbjct: 127 GGTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTG 186
Query: 190 LSGKVAV--MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
G V + + D L +LD A+KGC ++ + A+
Sbjct: 187 NGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230
>gnl|CDD|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome. The
MTR3 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 210
Score = 185 bits (471), Expect = 1e-58
Identities = 82/213 (38%), Positives = 125/213 (58%), Gaps = 4/213 (1%)
Query: 21 LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKV-HGSVLINFQYSMAVF 79
+R I + GV SQ+ GSAY+E GNTKV+ +VYGPRP+ ++ G + ++ A F
Sbjct: 1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKF--APF 58
Query: 80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
+T R+ + D + E+S L QA+ A+ E +P+SQID+FV VL++DG A + A
Sbjct: 59 ATPGRRRHGQ-DSEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITA 117
Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL 199
A+LAL DAGI M + V ACSA+L GD L+D + EE + +A +P +V +
Sbjct: 118 ASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGGVMLAYMPSLNQVTQLWQ 177
Query: 200 SQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
S ++ +D L LD + GC IH ++ A+ +
Sbjct: 178 SGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases. RNase
PH-like 3'-5' exoribonucleases are enzymes that catalyze
the 3' to 5' processing and decay of RNA substrates.
Evolutionarily related members can be fond in
prokaryotes, archaea, and eukaryotes. Bacterial
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 and is involved in mRNA degradation
in a 3'-5' direction. Archaeal exosomes contain two
individually encoded RNase PH-like 3'-5'
exoribonucleases and are required for 3' processing of
the 5.8S rRNA. The eukaryotic exosome core is composed
of six individually encoded RNase PH-like subunits, but
it is not a phosphorolytic enzyme per se; it directly
associates with Rrp44 and Rrp6, which are hydrolytic
exoribonucleases related to bacterial RNase II/R and
RNase D. All members of the RNase PH-like family form
ring structures by oligomerization of six domains or
subunits, except for a total of 3 subunits with tandem
repeats in the case of PNPase, with a central channel
through which the RNA substrate must pass to gain access
to the phosphorolytic active sites.
Length = 218
Score = 146 bits (370), Expect = 2e-43
Identities = 67/221 (30%), Positives = 102/221 (46%), Gaps = 22/221 (9%)
Query: 21 LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS 80
R + GV +Q+DGSA ++ GNTKV+ AV GP +K + + ++ +
Sbjct: 1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPD-KGTLYVNVEISPGA 59
Query: 81 TGERKTRPRGDRKTSEISLQLRQAVSAAIM---SEVHPRSQIDIFVEVLQADGGNFCACV 137
GER+ + + EIS L + + A+++ S P + + ++VL DGG AC
Sbjct: 60 VGERR-QGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACW 118
Query: 138 NAATLALIDAGIP-------------MREYVVACSASLAGD-TPLVDISHLEETLGGPNL 183
NAA AL DAGIP M++ +VA S D L+D + EE L L
Sbjct: 119 NAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEELADSTL 178
Query: 184 TVAALPLSGKVAVMELSQKLHLD--HLPRVLDCALKGCADI 222
TVA SGK+ ++ LD + L+ A K +
Sbjct: 179 TVAVDK-SGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
>gnl|CDD|216323 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 = 129
Score = 141 bits (357), Expect = 1e-42
Identities = 56/131 (42%), Positives = 73/131 (55%), Gaps = 2/131 (1%)
Query: 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
ELR I GV SQ+DGSA +E G+TKVLA V GP K L +Y + F
Sbjct: 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGEL-TVEYEESPF 59
Query: 80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
++GER R + E+S + +A+ +I E +PR +I I V VL DG A +NA
Sbjct: 60 ASGERP-EGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINA 118
Query: 140 ATLALIDAGIP 150
A+LAL DAGIP
Sbjct: 119 ASLALADAGIP 129
>gnl|CDD|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome. The
RRP46 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 199
Score = 124 bits (314), Expect = 3e-35
Identities = 53/158 (33%), Positives = 83/158 (52%), Gaps = 13/158 (8%)
Query: 21 LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL-INFQYSMAVF 79
LR + C LG+ S++DGSA QG+T VLAAVYGP V+ + + L + + +
Sbjct: 1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLP 60
Query: 80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
E+ + L LR + I+ +HPR+ I + ++VLQ DG +NA
Sbjct: 61 GVKEK-----------LLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINA 109
Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLV-DISHLEE 176
A LAL+DAG+PM+ A + ++ D ++ D + EE
Sbjct: 110 ACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEE 147
>gnl|CDD|206767 cd11362, RNase_PH_bact, Ribonuclease PH. Ribonuclease PH (RNase
PH)-like 3'-5' exoribonucleases are enzymes that
catalyze the 3' to 5' processing and decay of RNA
substrates. Structurally all members of this family form
hexameric rings (trimers of dimers). Bacterial RNase PH
forms a homohexameric ring, and removes nucleotide
residues following the -CCA terminus of tRNA.
Length = 227
Score = 75.7 bits (187), Expect = 2e-16
Identities = 55/176 (31%), Positives = 79/176 (44%), Gaps = 26/176 (14%)
Query: 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY----GPRPVRNKSIKVHGSVLINFQYS 75
+LR I G ++GS IE G+TKVL P +R K G + +YS
Sbjct: 1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGK-----GKGWVTAEYS 55
Query: 76 MAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEVLQADG 130
M ST ER R K T EI + +++ AA+ + + R I I +VLQADG
Sbjct: 56 MLPRSTHERTQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGER-TITIDCDVLQADG 114
Query: 131 GNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLE 175
G A + A +AL DA P++ +V A S + PL+D+ + E
Sbjct: 115 GTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDGEPLLDLDYEE 170
>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
[Transcription, RNA processing].
Length = 236
Score = 69.7 bits (171), Expect = 3e-14
Identities = 66/232 (28%), Positives = 104/232 (44%), Gaps = 26/232 (11%)
Query: 12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYG--PRPVRNKSIKVHGS 67
R DGR+ +LR + ++GS IE GNTKVL A+V P +R G
Sbjct: 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGS-----GE 55
Query: 68 VLINFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFV 123
I +Y M +T R R + +T EI + +A+ A + E I I
Sbjct: 56 GWITAEYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDC 115
Query: 124 EVLQADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDIS 172
+V+QADGG A + A +AL DA P+R++V A S + P++D+
Sbjct: 116 DVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGEPVLDLD 175
Query: 173 HLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPRVLDCALKGCADI 222
+ E++ ++ V G V V +++ D L ++LD A KG ++
Sbjct: 176 YEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIREL 227
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 63.2 bits (155), Expect = 7e-12
Identities = 54/187 (28%), Positives = 82/187 (43%), Gaps = 32/187 (17%)
Query: 12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYG--PRPVRNKSIKVHGS 67
R DGR +LR + ++GS +E G+TKVL A+V PR ++ + G
Sbjct: 2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQ-----GQ 56
Query: 68 VLINFQYSMAVFSTGERKTRP--RG--DRKTSEIS-L---QLRQAVSAAIMSEVHPRSQI 119
+ +Y M +T R R +G +T EI L LR V + E I
Sbjct: 57 GWVTAEYGMLPRATHTRNDREAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGE----RTI 112
Query: 120 DIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPL 168
I +V+QADGG A + A +AL DA P+++ V A S + P+
Sbjct: 113 TIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIVDGEPV 172
Query: 169 VDISHLE 175
+D+ + E
Sbjct: 173 LDLDYEE 179
>gnl|CDD|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide
nucleotidyltransferase, repeat 2. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and in
quality control of ribosomal RNA precursors, with the
second repeat containing the active site. PNPase is part
of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 223
Score = 56.0 bits (136), Expect = 2e-09
Identities = 54/177 (30%), Positives = 84/177 (47%), Gaps = 12/177 (6%)
Query: 20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGSVLINF--QYSM 76
E+R I C +G+ ++ GSA +G T+VL V G K + G F Y+
Sbjct: 1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60
Query: 77 AVFSTGE-RKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFC 134
+S GE + G R+ +L R A+ + S E P + I + EVL+++G +
Sbjct: 61 PPYSVGETGRVGGPGRREIGHGALAER-ALLPVLPSPEDFPYT-IRVVSEVLESNGSSSM 118
Query: 135 ACVNAATLALIDAGIPMREYVVACSASLAGDTP-----LVDISHLEETLGGPNLTVA 186
A V +LAL+DAG+P++ V + L + L DI LE+ LG + VA
Sbjct: 119 ASVCGGSLALMDAGVPIKAPVAGIAMGLITEGIDDYRVLTDILGLEDHLGDMDFKVA 175
>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome.
The RRP42 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA. It is required for 3'
processing of the 5.8S rRNA.
Length = 256
Score = 56.1 bits (136), Expect = 3e-09
Identities = 60/260 (23%), Positives = 97/260 (37%), Gaps = 66/260 (25%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-------YGPRPVRNKSI 62
G R DGR E R I GV +++GSA ++ GNT+VLA V + P N+
Sbjct: 15 GKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTP--NE-- 70
Query: 63 KVHGSVLINFQYS-MA--VFSTGERKTRP--------RGDRKTSEI---SLQLRQAVSAA 108
G +++N + +A F G RG R++ I L +
Sbjct: 71 ---GVLIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVW 127
Query: 109 IMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP------------------ 150
++ IDI+ VL DG F A AA AL++ +P
Sbjct: 128 VVF-------IDIY--VLDYDGNLFDASALAAVAALLNTKVPEYEVDENEVIEVLGEELP 178
Query: 151 --MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHL 208
+ V+ + + G +VD + EE + +T+ G + + QK
Sbjct: 179 LPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDE-DGNIVAL---QKGGGGSF 234
Query: 209 PR-----VLDCALKGCADIH 223
+D AL+ A++
Sbjct: 235 TEDEIDKAIDIALEKAAELR 254
>gnl|CDD|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome. The
RRP45 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 259
Score = 56.0 bits (136), Expect = 3e-09
Identities = 47/150 (31%), Positives = 62/150 (41%), Gaps = 28/150 (18%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
GLR DGR E R I+ F G + G T+VLA V P+P R
Sbjct: 16 GLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPN----E 68
Query: 66 GSVLINFQYS-MAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSE---VHPRS-- 117
G + IN + S MA S RP + E+S L +A+ S A+ +E +
Sbjct: 69 GILFINVELSPMA--SPAFEPGRPSEEEV--ELSRLLERALRDSRAVDTESLCIIAGEKV 124
Query: 118 -QIDIFVEVLQADGGNF--CACVNAATLAL 144
I + V VL GN A + AA AL
Sbjct: 125 WSIRVDVHVL-NHDGNLIDAASL-AAIAAL 152
>gnl|CDD|217696 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 = 68
Score = 50.6 bits (122), Expect = 7e-09
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 154 YVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL--SQKLHLDHLPRV 211
V A + ++D + EE+L +LT+ VA+M+ +L + L
Sbjct: 2 PVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLEA 61
Query: 212 LDCALKG 218
L+ A +G
Sbjct: 62 LELAHEG 68
>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 53.1 bits (128), Expect = 3e-08
Identities = 56/271 (20%), Positives = 96/271 (35%), Gaps = 56/271 (20%)
Query: 3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-------YGPR 55
+L G+R DGR E R + GV +++GSA ++ GNT+V+ V +
Sbjct: 15 ILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDT 74
Query: 56 PVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP--------RGDRKTSEI---SLQLRQA 104
P + V L F G RG R++ I L + +
Sbjct: 75 PNEG--VLVVNVELSPLASP--SFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEG 130
Query: 105 VSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------------- 150
+ V +D+ VL DG A AA AL++ +P
Sbjct: 131 KKVWV---VF----VDVH--VLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEV 181
Query: 151 --------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK 202
+ ++ + + G+ +VD S EE + LT+ + G++ ++
Sbjct: 182 EEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTI-TVNEDGEIVAIQKVGG 240
Query: 203 LHLDH--LPRVLDCALKGCADIHAILDTAIK 231
+ L + L AL + L A+K
Sbjct: 241 GSITESDLEKALKTALSKAEKLREALKEALK 271
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 53.3 bits (129), Expect = 4e-08
Identities = 61/188 (32%), Positives = 88/188 (46%), Gaps = 23/188 (12%)
Query: 7 YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIK-V 64
G +R DGR G E+R I +GV ++ GSA +G T+ L V G P + I +
Sbjct: 308 LEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGT-PRDAQVIDIL 366
Query: 65 HGSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQI 119
G F Y+ FS GE T G EI +L R A++ + SE I
Sbjct: 367 EGEYKKRFLLHYNFPPFSVGE--TGRMGSPGRREIGHGALAER-ALAPVLPSEEEFPYTI 423
Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA------GDTPLV--DI 171
+ E+L+++G + A V +LAL+DAG+P++ V A +A GD V DI
Sbjct: 424 RVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPV----AGIAMGLIKEGDKYAVLSDI 479
Query: 172 SHLEETLG 179
E+ LG
Sbjct: 480 LGDEDHLG 487
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 52.1 bits (125), Expect = 1e-07
Identities = 71/244 (29%), Positives = 101/244 (41%), Gaps = 39/244 (15%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAA-----------VYGPRPV 57
G+R DGR ++R + + V + GSA E+G T++L + P
Sbjct: 333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPE 392
Query: 58 RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
+K H Y+ +STGE T G K EI +L R V E
Sbjct: 393 TSKRYMHH--------YNFPPYSTGE--TGRVGSPKRREIGHGALAERALVPVLPSREEF 442
Query: 115 PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT-------- 166
P + I E L ++G V A+TL+L++AG+P++ V + L D
Sbjct: 443 PYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGETRYV 501
Query: 167 PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLP-RVLDCALKGCADIH-A 224
L DI E+ G + VA S V ++L K LD +P VL ALK D A
Sbjct: 502 ALTDILGAEDAFGDMDFKVAG--TSEFVTALQLDTK--LDGIPASVLASALKQARDARLA 557
Query: 225 ILDT 228
ILD
Sbjct: 558 ILDV 561
>gnl|CDD|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome. The
RRP43 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 261
Score = 50.2 bits (121), Expect = 2e-07
Identities = 52/233 (22%), Positives = 77/233 (33%), Gaps = 60/233 (25%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
+R DGR E R +G S +DGSA ++ GNT VL + P
Sbjct: 16 NVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPD----E 71
Query: 66 GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIF-- 122
G ++ N + S+ R P SE + L ++ + S V Q+ I
Sbjct: 72 GYLVPNVDLP-PLCSSKFRPGPP------SEEAQVLSSFLADILLNSNVLDLEQLCIVPG 124
Query: 123 ---------VEVLQADGGNFCACVNAATLALIDAGIP-------MREYVV---------- 156
V L DG A + A AL + +P VV
Sbjct: 125 KLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTIDEETELVVVNPEERRPLNL 184
Query: 157 ---ACSASLA---GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKL 203
S + A L D + EE L +TV V++ + +L
Sbjct: 185 KNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTV----------VVDENGEL 227
>gnl|CDD|234271 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)
[Transcription, Degradation of RNA].
Length = 684
Score = 49.4 bits (119), Expect = 9e-07
Identities = 48/156 (30%), Positives = 74/156 (47%), Gaps = 15/156 (9%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSI--KVH 65
G R DGR +R I +GV ++ GSA +G T+ L G R++ I +
Sbjct: 308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTE--RDEQIIDDLE 365
Query: 66 GSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMS-EVHPRSQI 119
G F Y+ +S GE G EI +L R A+ A + S E P + I
Sbjct: 366 GEYRKRFMLHYNFPPYSVGE--VGRVGGPGRREIGHGALAER-ALKAVLPSEEEFPYT-I 421
Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV 155
+ E+L+++G + A V +LAL+DAG+P++ V
Sbjct: 422 RVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPV 457
>gnl|CDD|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome. The
RRP42 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 272
Score = 48.0 bits (115), Expect = 1e-06
Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 19/153 (12%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
+RNDGR + R I GV S ++GSA + GNT VL V P P
Sbjct: 17 NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPET------P 70
Query: 66 GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSE-----VHPRSQI- 119
+ F + ++ E + R G+ +E+S L +A+ + + + P Q
Sbjct: 71 NKGRLEFFVDCSPNASPEFEGR-GGEELATELSSALERALKSGSAIDLSKLCIVPGKQCW 129
Query: 120 DIFVEVL-QADGGNFCACVNAAT-LALIDAGIP 150
++V+VL GGN ++ A AL + IP
Sbjct: 130 VLYVDVLVLESGGNLLDAISIAVKAALFNTRIP 162
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 47.2 bits (112), Expect = 5e-06
Identities = 49/192 (25%), Positives = 81/192 (42%), Gaps = 14/192 (7%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKS---IKV 64
GG R+DGR E+R I G+ ++ GSA +G T+ LA V G + + + +
Sbjct: 436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDA 495
Query: 65 HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
QYS GE R+ + +A+ + SE I +
Sbjct: 496 DEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVEST 555
Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT--------PLV--DISHL 174
+ +++G + A V LAL DAG+P++ + + + DT PL+ DI+
Sbjct: 556 ITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGS 615
Query: 175 EETLGGPNLTVA 186
E+ G + VA
Sbjct: 616 EDASGDMDFKVA 627
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 45.3 bits (108), Expect = 1e-05
Identities = 20/42 (47%), Positives = 27/42 (64%)
Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV 51
G R DGR+ E R I GV +++GSA ++ GNT+VLA V
Sbjct: 23 GKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64
Score = 33.3 bits (77), Expect = 0.083
Identities = 27/139 (19%), Positives = 54/139 (38%), Gaps = 31/139 (22%)
Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIP--------------------MREYVVAC 158
ID++V L DG A + AA AL++ +P + + V
Sbjct: 139 IDVYV--LDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVTV 196
Query: 159 SASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVLD 213
+ + G+ +VD + EE++ +T+ G + + QK + + + +D
Sbjct: 197 TFAKIGNYLIVDPTLEEESVMDARITITTDE-DGNIVAI---QKSGIGSFTEEEVDKAID 252
Query: 214 CALKGCADIHAILDTAIKQ 232
AL+ ++ L A+
Sbjct: 253 IALEKAKELREKLKEALGI 271
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 37.7 bits (89), Expect = 0.006
Identities = 47/162 (29%), Positives = 74/162 (45%), Gaps = 27/162 (16%)
Query: 9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-----------GPRPV 57
G+R DGR+ E+R I +GV ++ GSA +G T+ L G
Sbjct: 312 EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGE 371
Query: 58 RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMS-EV 113
K +H Y+ +S GE T G EI +L R A+ + S E
Sbjct: 372 YKKRFMLH--------YNFPPYSVGE--TGRVGSPGRREIGHGALAER-ALEPVLPSEEE 420
Query: 114 HPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV 155
P + I + E+L+++G + A V ++LAL+DAG+P++ V
Sbjct: 421 FPYT-IRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPV 461
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 33.4 bits (76), Expect = 0.14
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 203 LHLDHLPRVLDCALKGCADIHAILDTAIKQ----HLIKVAGARGLGRK------FQLGQL 252
+ LD +P+ L C K ++H L++ IKQ ++ ++G G G+ QL Q
Sbjct: 748 MQLDVVPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQH 807
Query: 253 TGKKK 257
K+K
Sbjct: 808 KTKQK 812
>gnl|CDD|183423 PRK12306, uvrC, excinuclease ABC subunit C; Reviewed.
Length = 519
Score = 31.6 bits (72), Expect = 0.41
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 192 GKVAVMELSQKLHLDHLPRVLDC 214
++ + EL KLHL P V++C
Sbjct: 349 DEIKLEELKNKLHLPKPPNVIEC 371
>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide
nucleotidyltransferase, repeat 1. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and
in quality control of ribosomal RNA precursors. It is
part of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 229
Score = 27.9 bits (63), Expect = 4.8
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 33 QSDGSAYIEQGNTKVLAAV 51
Q+DGS ++ G+T VL
Sbjct: 22 QADGSVVVQYGDTVVLVTA 40
>gnl|CDD|107206 cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate
(PLP) dependent enzyme that catalyses the last reaction
in the synthesis of threonine from aspartate. It
proceeds by converting O-phospho-L-homoserine (OPH) into
threonine and inorganic phosphate. In plants, OPH is an
intermediate between the methionine and
threonine/isoleucine pathways. Thus threonine synthase
competes for OPH with cystathionine-gamma-synthase, the
first enzyme in the methionine pathway. These enzymes
are in general dimers. Members of this CD, Thr-synth_1,
are widely distributed in bacteria, archaea and higher
plants.
Length = 324
Score = 27.6 bits (62), Expect = 6.5
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 164 GDTPLVDISHLEETLGGPNL 183
G+TPLV L E LGG NL
Sbjct: 21 GNTPLVRAPRLGERLGGKNL 40
>gnl|CDD|223088 COG0009, SUA5, Putative translation factor (SUA5) [Translation,
ribosomal structure and biogenesis].
Length = 211
Score = 27.6 bits (62), Expect = 6.5
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 5/44 (11%)
Query: 138 NAATLALIDA-GIPMREYVVACSASLAGDTPLVDISHLEETLGG 180
+ LALI+A G P+ + SA+L+G + GG
Sbjct: 125 HPIALALIEALGEPL----ASTSANLSGQPSPTTAEEVRADFGG 164
>gnl|CDD|236527 PRK09462, fur, ferric uptake regulator; Provisional.
Length = 148
Score = 27.0 bits (60), Expect = 6.9
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 191 SGKVAVMELSQKLHLDHLPRVLDC 214
GK +V EL+Q+ H DHL LDC
Sbjct: 75 GGK-SVFELTQQHHHDHLI-CLDC 96
>gnl|CDD|133020 cd02540, GT2_GlmU_N_bac, N-terminal domain of bacterial GlmU. The
N-terminal domain of N-Acetylglucosamine-1-phosphate
uridyltransferase (GlmU). GlmU is an essential bacterial
enzyme with both an acetyltransferase and an
uridyltransferase activity which have been mapped to the
C-terminal and N-terminal domains, respectively. This
family represents the N-terminal uridyltransferase. GlmU
performs the last two steps in the synthesis of
UDP-N-acetylglucosamine (UDP-GlcNAc), which is an
essential precursor in both the peptidoglycan and the
lipopolysaccharide metabolic pathways in Gram-positive
and Gram-negative bacteria, respectively.
Length = 229
Score = 27.5 bits (62), Expect = 7.4
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 147 AGIPMREYVVACSASLAGDTPLVDISH----LEETLGGPNLTVA 186
AG PM E+V+ + +L D +V + H +++ L PN+
Sbjct: 24 AGKPMLEHVLDAARALGPDRIVVVVGHGAEQVKKALANPNVEFV 67
>gnl|CDD|218105 pfam04479, RTA1, RTA1 like protein. This family is comprised of
fungal proteins with multiple transmembrane regions.
RTA1 is involved in resistance to 7-aminocholesterol,
while RTM1 confers resistance to an an unknown toxic
chemical in molasses. These proteins may bind to the
toxic substance, and thus prevent toxicity. They are not
thought to be involved in the efflux of xenobiotics.
Length = 226
Score = 27.4 bits (61), Expect = 7.8
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 120 DIFVEVLQADGGNFCACVNAATLA--LIDAGI 149
D+ VLQA GG + + T LI AG+
Sbjct: 80 DVISLVLQAAGGGLMSKATSTTTGSHLITAGL 111
>gnl|CDD|224665 COG1751, COG1751, Uncharacterized conserved protein [Function
unknown].
Length = 186
Score = 27.1 bits (60), Expect = 8.0
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALIDAG-IPMREYVVACSASLAG-DTPLV 169
S ++I E L+ G CV +A DAG IP+ E V+A + G DT LV
Sbjct: 108 SPLEIIAETLRMFGQGVKVCVEITIMA-ADAGLIPVSEEVIAIGGTERGADTALV 161
>gnl|CDD|173855 cd08490, PBP2_NikA_DppA_OppA_like_3, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 470
Score = 27.6 bits (62), Expect = 8.2
Identities = 21/84 (25%), Positives = 31/84 (36%), Gaps = 25/84 (29%)
Query: 39 YIEQGNTKVLAA-------VYGPRPV------RNKSIKVHGSVLINFQYSMAVFSTGERK 85
+I NT+ LA YG P ++ KV SV + +T +
Sbjct: 185 FIPDANTRALALQSGEVDIAYGLPPSSVERLEKDDGYKVS-SVPT-PRTYFLYLNTEKG- 241
Query: 86 TRPRGDRKTSEISLQLRQAVSAAI 109
P D + +RQA+S AI
Sbjct: 242 --PLADVR-------VRQALSLAI 256
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.387
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,168,990
Number of extensions: 1245312
Number of successful extensions: 967
Number of sequences better than 10.0: 1
Number of HSP's gapped: 936
Number of HSP's successfully gapped: 49
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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: 58 (26.1 bits)