RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15057
(151 letters)
>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 = 204 bits (522), Expect = 3e-68
Identities = 74/146 (50%), Positives = 108/146 (73%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
LR L +L +LSR+DGS FSQG T V+A++YGP+E K++K + D+A++EVI RPKSGL
Sbjct: 1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLP 60
Query: 64 FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
V+++L E +++ST E +L LHPRT + + +Q LQD GSLL+C INAACLAL+++G+
Sbjct: 61 GVKEKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVP 120
Query: 124 MRYILAAVSCIINDKNEVILDANQIQ 149
M+ + AAV+C I + E+ILD +
Sbjct: 121 MKGLFAAVTCAITEDGEIILDPTAEE 146
>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 = 110 bits (278), Expect = 4e-31
Identities = 54/162 (33%), Positives = 85/162 (52%), Gaps = 25/162 (15%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKASVEVIF------ 56
LR ++ ++ + S +DGS QG T V+A++YGP E + + + D+A V +
Sbjct: 12 LRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVNCEYSMATFS 71
Query: 57 ------RPKSGLSFVQD-RLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
R K D R E I+ T E+ +LT L+PR+ + + +Q LQ G LL+
Sbjct: 72 TGERKRRGKG------DRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLA 125
Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILDANQI 148
CINAA LALI++GI M+ + A S ++ +LD N +
Sbjct: 126 ACINAATLALIDAGIPMKDYVCACSAGYLDSTP--LLDLNYL 165
>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 = 88.4 bits (220), Expect = 2e-23
Identities = 34/127 (26%), Positives = 60/127 (47%), Gaps = 8/127 (6%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
LR ++ + +LS++DGS + G T V+A++ GP+E ++ + V + S
Sbjct: 2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFAS 61
Query: 64 F--------VQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACL 115
++ +I ++ +PR + + + L D GSLL INAA L
Sbjct: 62 GERPEGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINAASL 121
Query: 116 ALINSGI 122
AL ++GI
Sbjct: 122 ALADAGI 128
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 89.3 bits (222), Expect = 9e-23
Identities = 40/151 (26%), Positives = 66/151 (43%), Gaps = 10/151 (6%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKA--SVEVIFRP 58
D LR +K +L ++GS + G T V+ ++ GP E K + E P
Sbjct: 16 DELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLP 75
Query: 59 KSGLS-----FVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCIN 111
+S + R KE +I + + L P +++ + LQ G + I
Sbjct: 76 RSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASIT 135
Query: 112 AACLALINSGISMRYILAAVSCIINDKNEVI 142
A LAL ++GI +R ++AA+S I D V+
Sbjct: 136 GASLALADAGIPLRDLVAAISVGIVDGVIVL 166
>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 81.2 bits (201), Expect = 2e-19
Identities = 48/163 (29%), Positives = 79/163 (48%), Gaps = 18/163 (11%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--P 58
D LR +K ++ +L +DGS G ++A++YGP E + + D+A + V + P
Sbjct: 22 DELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAP 81
Query: 59 KSGLSFVQDRLK----------ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
S V +R + VI+ E A++ L PRT + + I+ LQ
Sbjct: 82 FS----VDERKRPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVA 137
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
I AA LAL ++GI MR ++A + D ++LD N+ + N
Sbjct: 138 GITAASLALADAGIPMRDLVAGCAVGKVD-GVIVLDLNKEEDN 179
>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 = 78.3 bits (193), Expect = 1e-18
Identities = 48/160 (30%), Positives = 80/160 (50%), Gaps = 12/160 (7%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIF---- 56
D LR +K + +L +DGS G T ++A++YGP EA + + D+A + V +
Sbjct: 16 DELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAVLRVRYHMAP 75
Query: 57 -----RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCIN 111
R + G S + + + VI+ E A+L PRT + + I+ LQ G +
Sbjct: 76 FSTDERKRPGPSRREIEISK-VIREALEPAILLEQFPRTVIDVFIEVLQADGGTRCAGLT 134
Query: 112 AACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
AA LAL ++GI MR ++ V+ D V+LD ++ +
Sbjct: 135 AASLALADAGIPMRDLVVGVAVGKVD-GVVVLDLSEEEDM 173
>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 = 76.2 bits (188), Expect = 7e-18
Identities = 39/168 (23%), Positives = 70/168 (41%), Gaps = 24/168 (14%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
R ++ + +L+++DGS + G T V+ ++ GP+ + DK ++ V G
Sbjct: 1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAV 60
Query: 64 FVQ------DRLKE--SVIKSTCESA---LLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
+ D E +++ T E++ + P + + IQ L G LL C NA
Sbjct: 61 GERRQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNA 120
Query: 113 ACLALINSGI-------------SMRYILAAVSCIINDKNEVILDANQ 147
A AL ++GI M+ ++ AVS ++LD
Sbjct: 121 AIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTG 168
>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 = 71.6 bits (176), Expect = 4e-16
Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 20/157 (12%)
Query: 4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--PKS 60
LR +K ++ +L +DGS G ++A++YGP E + + D+A + V + P S
Sbjct: 2 LRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFS 61
Query: 61 GLSFVQDRLK----------ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
V +R + VIK E A++ PRT++ + ++ LQ +
Sbjct: 62 ----VDERKRPGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGL 117
Query: 111 NAACLALINSGISMRYILAAVSC-IINDKNEVILDAN 146
NAA LAL ++GI MR ++AA + ++ K ++LD N
Sbjct: 118 NAASLALADAGIPMRDLVAACAAGKVDGK--IVLDLN 152
>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 = 59.1 bits (144), Expect = 2e-11
Identities = 38/143 (26%), Positives = 71/143 (49%), Gaps = 9/143 (6%)
Query: 10 QLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA--SVEVIFRP------KSG 61
+ ++S++ GS G T V+ S+YGP + D+ + EV F P +
Sbjct: 7 KTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPGRRRH 66
Query: 62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
++R S++ E A+ +P++ + + + L+ GS+L+ I AA LAL ++G
Sbjct: 67 GQDSEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAG 126
Query: 122 ISMRYILAAVSCIINDKNEVILD 144
I M ++ A S + +E++LD
Sbjct: 127 IEMYDLVTACSAALIG-DELLLD 148
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 32.9 bits (75), Expect = 0.051
Identities = 35/148 (23%), Positives = 63/148 (42%), Gaps = 20/148 (13%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQT--VVVASMYGPVEAKIQKTIID-----KASVEV 54
D +R + S +L R+ GS +F++G+T + V ++ A+ ++D + ++
Sbjct: 446 DEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQY 505
Query: 55 IFRPKS----GLSFVQDRLKESVIKSTCESALLTMLHPRTS------VILTIQELQDQGS 104
F P G R +E E AL +L V TI E S
Sbjct: 506 SFPPSCVGEVGRIGAPSR-REIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSS 564
Query: 105 LLSCCINAACLALINSGISMRYILAAVS 132
+ S C CLAL ++G+ ++ +A ++
Sbjct: 565 MASVC--GGCLALQDAGVPVKCPIAGIA 590
>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 = 28.7 bits (65), Expect = 1.2
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVA 32
D R+++ + ++ +++GS + G T V+A
Sbjct: 24 DEYRDIEIETGVIPKAEGSALVKLGNTQVLA 54
>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 = 28.3 bits (64), Expect = 1.5
Identities = 9/30 (30%), Positives = 20/30 (66%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVA 32
+R + ++ +L R+ GS +F++G+T V+
Sbjct: 1 EIRPISCEVGLLPRTHGSALFTRGETQVLC 30
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 28.4 bits (64), Expect = 1.6
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 10 QLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVI-----FRPKSGLSF 64
+L+I+ +DG IF++G + V K+ K +IDK V + L
Sbjct: 510 ELSIIVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVK 569
Query: 65 VQDRLKESVIK 75
+ D+LK IK
Sbjct: 570 LLDKLKNLGIK 580
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 27.1 bits (61), Expect = 3.1
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVA 32
D R ++ + ++ +++GS + G T V+A
Sbjct: 32 DEYRPIEIETGVIKKAEGSALVKLGNTQVLA 62
>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 27.3 bits (61), Expect = 3.1
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS 33
D R L+ + ++ +++GS + G T VV
Sbjct: 31 DEFRPLEIETGVIPKANGSALVKLGNTQVVVG 62
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 26.6 bits (60), Expect = 6.9
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQT---VVV 31
D +R + ++ +L R+ GS +F++G+T VV
Sbjct: 322 DEIRPISIEVGVLPRTHGSALFTRGETQALVVA 354
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 26.4 bits (59), Expect = 7.4
Identities = 12/40 (30%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 5 RELKSQLNILSRSDGSVIFSQGQT--VVVASMYGPVEAKI 42
R + ++ +L R+ GS +F++G+T +VV ++ P +A++
Sbjct: 323 RPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQV 362
>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 = 26.0 bits (58), Expect = 8.1
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 3 SLRELKSQLNILSRSDGSVIFSQGQTVVVAS 33
LR + ++GSV+ G T V+ +
Sbjct: 1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCT 31
>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 = 26.3 bits (59), Expect = 8.7
Identities = 9/27 (33%), Positives = 20/27 (74%)
Query: 2 DSLRELKSQLNILSRSDGSVIFSQGQT 28
D++R + ++ +L R+ GS +F++G+T
Sbjct: 318 DTIRPISIEVGVLPRTHGSALFTRGET 344
>gnl|CDD|185600 PTZ00410, PTZ00410, NAD-dependent SIR2; Provisional.
Length = 349
Score = 26.0 bits (57), Expect = 8.9
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 90 TSVILTIQELQDQGSLLSCC---INAACLALINSGISMRYIL------AAVSCI 134
T+V I+ L D+G LL CC I+ A +G+ ++ +A SCI
Sbjct: 101 TAVHHFIRLLADEGRLLRCCTQNIDGLERA---AGVPPSLLVEAHGSFSAASCI 151
>gnl|CDD|220428 pfam09826, Beta_propel, Beta propeller domain. Members of this
family comprise secreted bacterial proteins containing
C-terminal beta-propeller domain distantly related to
WD-40 repeats.
Length = 521
Score = 26.1 bits (58), Expect = 9.5
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 18 DGSVIF-SQGQTVVVASMYGPVEAKIQKTI 46
DG I+ G + + Y E KI I
Sbjct: 21 DGKYIYVVSGGRLYIVDAYPAEELKIVSEI 50
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 0.131 0.353
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,033,021
Number of extensions: 603671
Number of successful extensions: 520
Number of sequences better than 10.0: 1
Number of HSP's gapped: 511
Number of HSP's successfully gapped: 27
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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: 54 (24.5 bits)