RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9088
(756 letters)
>gnl|CDD|192357 pfam09741, DUF2045, Uncharacterized conserved protein (DUF2045).
This entry is the conserved 250 residues of proteins of
approximately 450 amino acids. It contains several
highly conserved motifs including a CVxLxxxD motif.The
function is unknown.
Length = 237
Score = 349 bits (898), Expect = e-116
Identities = 132/239 (55%), Positives = 165/239 (69%), Gaps = 8/239 (3%)
Query: 70 QGTSYWTDLFVRYFLFQTDS--NIDCDDLLFFVRKKYIKTSSRNLPKFETEVEVFRKDSR 127
+++WT +F YF+ +S D DDLLFFVR+K SSR L + E E EV+R+DS
Sbjct: 3 MDSNFWTGVFDVYFVRCMESRRRQD-DDLLFFVRRKLSCKSSRGLTENEDEPEVYRRDSP 61
Query: 128 KLP-IGDPDVDWEETVYLNMIIHQFDYTLTLAICTRTSPKHLQVLKRHSQKVYASPSRRR 186
KLP +GDPDVDWEE+VYLN+I H DYT+T+AICTR + K L + + SQ VYASPSR
Sbjct: 62 KLPELGDPDVDWEESVYLNLIAHTLDYTVTVAICTREALKTLSPIYKVSQTVYASPSRFH 121
Query: 187 MDTKGEVEEMTYPCVCFTVDNFNEVFHDILVRDGEMVCVELVASDRAGSVKSVIFLGSIR 246
MD+KGEVE + YP +CF VD+F+EVF D++V DGEMVCVELVA D + VIF GSIR
Sbjct: 122 MDSKGEVETIAYPEICFMVDDFDEVFDDVVVTDGEMVCVELVAHDTVKDPQGVIFSGSIR 181
Query: 247 YDALKRVYDAR-TSVSNKFTQRMSFGIFSNNSNSRIEFVKMKGPQGKGFAEMAVTKPKG 304
Y ALK+VYD R + ++ Q MSFG + EFV+MKGPQGKG AEMAV+
Sbjct: 182 YQALKKVYDGRRSRFGSRMAQLMSFGHI---KTGKAEFVRMKGPQGKGHAEMAVSGVVD 237
>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 = 265 bits (679), Expect = 2e-83
Identities = 81/148 (54%), Positives = 116/148 (78%)
Query: 456 VLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESK 515
VLAQVSC +V PK RPNEG+LFIN ELSPMASP FE GR ++ V ++R LE+ ++S+
Sbjct: 50 VLAQVSCEIVEPKPDRPNEGILFINVELSPMASPAFEPGRPSEEEVELSRLLERALRDSR 109
Query: 516 CIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQIII 575
+D ESLC++A EKVW++RVD++VLN+DGNL+ S+AA+AAL HFR PDVT G+++ +
Sbjct: 110 AVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGEEVTV 169
Query: 576 HSAAEKDPIPMTILHYPVTISYAVFNGG 603
HS E++P+P++I H P+ +++A F+ G
Sbjct: 170 HSPEEREPVPLSIHHIPICVTFAFFDDG 197
>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation,
ribosomal structure and biogenesis].
Length = 272
Score = 149 bits (378), Expect = 2e-40
Identities = 64/168 (38%), Positives = 102/168 (60%), Gaps = 7/168 (4%)
Query: 437 SISAENGEAVWCPWVK--PSEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETG 494
I NG A+ VK ++V+ V + P PNEG+L +N ELSP+ASP FE G
Sbjct: 42 VIPKANGSAL----VKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASPSFEPG 97
Query: 495 RQTDTSVMINRFLEKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAA 554
+ ++ ++R +++ +ESK IDLE LC+ +KVW V VD++VL+YDGNL+ S+AA
Sbjct: 98 PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAA 157
Query: 555 LAALAHFRHPDVTSTGDQIIIHSAAEKDPIPMTILHYPVTISYAVFNG 602
+AAL + R P GD I+ E++P+P+ + + P+++++A
Sbjct: 158 VAALLNTRVPKAVEVGDGEIVIE-VEEEPVPLPVSNPPISVTFAKIGN 204
>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 = 125 bits (315), Expect = 5e-32
Identities = 61/167 (36%), Positives = 93/167 (55%), Gaps = 9/167 (5%)
Query: 438 ISAENGEAVWCPWVK--PSEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGR 495
I G A VK ++VLA V + P PNEG+L +NAEL P+ASP FE G
Sbjct: 36 IPKAEGSA----LVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASPTFEPGP 91
Query: 496 QTDTSVMINRFLEKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAAL 555
+ ++ + R +++ +ESK IDLE L + +KVW V +D+ VL+YDGNL ++AA+
Sbjct: 92 PDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAV 151
Query: 556 AALAHFRHPDVTSTGDQIIIHSAAEKDPIPMTILHYPVTISYAVFNG 602
AAL + + P + +I E+ P+P+ PV+++ A G
Sbjct: 152 AALLNTKVP-EYEVDENEVIEVLGEELPLPVN--TLPVSVTVAKIGG 195
>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 = 122 bits (309), Expect = 3e-31
Identities = 46/151 (30%), Positives = 81/151 (53%), Gaps = 5/151 (3%)
Query: 456 VLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESK 515
VL + + P A P+EG L N +L P+ S +F G ++ + +++ FL S
Sbjct: 53 VLCGIKAEVATPAADTPDEGYLVPNVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSN 112
Query: 516 CIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTST--GDQI 573
+DLE LC+V + W + D+ L+YDGNLL +A +AAL + R P VT + +
Sbjct: 113 VLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTIDEETELV 172
Query: 574 IIHSAAEKDPIPMTILHYPVTISYAVFNGGS 604
+++ ++ P+ + + PV+ ++AVF+
Sbjct: 173 VVN---PEERRPLNLKNLPVSTTFAVFDDKH 200
>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 121 bits (306), Expect = 9e-31
Identities = 57/155 (36%), Positives = 89/155 (57%), Gaps = 5/155 (3%)
Query: 450 WVK--PSEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFL 507
VK ++VLA V + P PNEG+L +NAEL P+ASP FE G + ++ + R +
Sbjct: 52 LVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTFEPGPPDENAIELARVV 111
Query: 508 EKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVT 567
++ +ESK IDLE L + +KVW V +D+ VL++DGNLL +AA+AAL + + P V
Sbjct: 112 DRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVE 171
Query: 568 STGDQIIIHSAAEKDPIPMTILHYPVTISYAVFNG 602
D ++ + P+ + PVT+++A
Sbjct: 172 EGEDGVVDK---LGEDFPLPVNDKPVTVTFAKIGN 203
>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 = 110 bits (278), Expect = 1e-27
Identities = 44/149 (29%), Positives = 68/149 (45%), Gaps = 16/149 (10%)
Query: 456 VLAQVSCNMVIP-KATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKES 514
V+ V+ +V P K RP++G L++N E+SP A + G D + I+R LE+ + S
Sbjct: 27 VICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLERTIEAS 86
Query: 515 KCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQII 574
+D + W + VD+ VL+ DG LL C AA+AAL P V
Sbjct: 87 VILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVF------- 134
Query: 575 IHSAAEKDPIPMTILHYPVTISYAVFNGG 603
E+ P + + V +S + G
Sbjct: 135 ---VDERSPPLLLMKDLIVAVSVGGISDG 160
>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 = 103 bits (258), Expect = 3e-24
Identities = 43/118 (36%), Positives = 61/118 (51%)
Query: 454 SEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
++VL V + P PN+G L + SP ASP+FE + + ++ LE+ K
Sbjct: 52 TDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNASPEFEGRGGEELATELSSALERALKS 111
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGD 571
IDL LC+V ++ W + VD+ VL GNLL SIA AAL + R P V + D
Sbjct: 112 GSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSED 169
>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 = 93.4 bits (233), Expect = 1e-22
Identities = 32/111 (28%), Positives = 54/111 (48%), Gaps = 9/111 (8%)
Query: 455 EVLAQVSCNMVIPKATRPNE-GLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
+VLA V+ + P+ R G L + E SP AS + GR ++ + ++R +++ +
Sbjct: 27 KVLATVTGPIEPPQKERDFFPGELTVEYEESPFASGERPEGRPSEREIELSRLIDRALRP 86
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHP 564
S ++ W +R+D+ VL+ DG+LL AA ALA P
Sbjct: 87 SIPLEGY--------PRWEIRIDVTVLSDDGSLLDAAINAASLALADAGIP 129
>gnl|CDD|218906 pfam06130, PduL, Propanediol utilisation protein PduL. This family
consists of several bacterial propanediol utilisation
protein (PduL) sequences. The exact role of this protein
in propanediol utilisation is unknown. Sequences
containing this domain usually have two tandem copies
(Bateman A, pers. obs.).
Length = 70
Score = 32.8 bits (76), Expect = 0.063
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 217 VRDGEMVCVELVASDRAGSVKSVIFLGSIRY 247
+DG+ V VE + R G ++V G R+
Sbjct: 23 GQDGQFVAVETLVGPRGGIFENVRVRGPERF 53
>gnl|CDD|215802 pfam00224, PK, Pyruvate kinase, barrel domain. This domain of the
is actually a small beta-barrel domain nested within a
larger TIM barrel. The active site is found in a cleft
between the two domains.
Length = 348
Score = 31.9 bits (73), Expect = 1.2
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 13/79 (16%)
Query: 601 NGGSEGSTVPGFTECIQLDTALALSQDRQKLGVDSAYANLVNKT---DRILLDEG----- 652
+G + G + D A + D++K+ VD Y NL IL+D+G
Sbjct: 79 DGKKDIELKAGDKFLVSTDPAYKGAGDKEKIYVD--YKNLTKDVSPGGIILVDDGVLSLK 136
Query: 653 --EKDSGET-KVKVEKVGP 668
EKD +T +V G
Sbjct: 137 VLEKDDDKTLVTEVLNGGV 155
>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and
biogenesis].
Length = 230
Score = 31.5 bits (72), Expect = 1.4
Identities = 26/111 (23%), Positives = 39/111 (35%), Gaps = 21/111 (18%)
Query: 459 QVSCNMVIPKATRP----NEGLLFINAELSPMASPQFETGRQTD------TSVMINRFLE 508
+V C + P+ P G ++ AE M T + + I+R +
Sbjct: 43 KVICTVSGPREPVPRFLRGTGKGWLTAEYG-MLP--RSTDERKKREADRGRTKEISRLIG 99
Query: 509 KCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALA 559
+ IDLE L E + +D +VL DG A ALA
Sbjct: 100 RAL--RAVIDLELL---PESTID---IDCDVLQADGGTRTASITGASLALA 142
>gnl|CDD|214331 CHL00002, matK, maturase K.
Length = 504
Score = 31.0 bits (71), Expect = 2.8
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 81 RYFLFQTDSNI-DCDDLLFFVRKK--YIK-TSSRNLP-------KFETEVEVFRKDSRK 128
R FLF +S + + + + F+RK+ +++ TSS K E VEVFR D +K
Sbjct: 205 RLFLFLYNSYVCEYESIFVFLRKQSSHLRSTSSGVFLERIHFYGKIEHLVEVFRNDFQK 263
>gnl|CDD|202484 pfam02953, zf-Tim10_DDP, Tim10/DDP family zinc finger. Putative
zinc binding domain with four conserved cysteine
residues. This domain is found in the human disease
protein TIMM8A. Members of this family such as Tim9 and
Tim10 are involved in mitochondrial protein import.
Members of this family seem to be localised to the
mitochondrial intermembrane space.
Length = 66
Score = 28.0 bits (63), Expect = 2.8
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 502 MINRFLEKCFKESKCID 518
+IN+ E CFK KC+
Sbjct: 16 LINKLTENCFK--KCVT 30
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The
topoisomerase-primase (TORPIM) nucleotidyl
transferase/hydrolase domain found in the active site
regions of proteins similar to Escherichia coli DnaG.
Primases synthesize RNA primers for the initiation of
DNA replication. DnaG type primases are often closely
associated with DNA helicases in primosome assemblies.
The TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function. E. coli DnaG is a single
subunit enzyme.
Length = 79
Score = 28.2 bits (64), Expect = 3.7
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 146 MIIHQFDYTLTLAIC-TRTSPKHLQVLKRHSQKVY 179
+ +HQ +A T + + ++LKR +++V
Sbjct: 13 IALHQAGIKNVVASLGTALTEEQAELLKRLAKEVI 47
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 30.2 bits (68), Expect = 4.0
Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 13/118 (11%)
Query: 318 ETDMWD-SDWDDDPEDFYYYRHQRRLSDPSANI--------NMFAKSIWKGPVNKTTAKA 368
E D W+ WD + + Y + S P + M AK G + AKA
Sbjct: 84 EFDFWNRPSWDTEDISTHNYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKA 143
Query: 369 VSEDEGLDSLAHG-VAEIEAGDMRDELDDGAYNPLWTMRGFTQTFHFWKESKRAQDWT 425
E + + A VAE+ R L D + + +R + +H + +K A T
Sbjct: 144 FDESHQVSATAAAKVAELSK---RIGLTDKIFAGMEAVRSVDEKYHVSEFTKSAATAT 198
>gnl|CDD|234067 TIGR02943, Sig70_famx1, RNA polymerase sigma-70 factor, TIGR02943
family. This group of sigma factors are members of the
sigma-70 family (TIGR02937). They and appear by
homology, tree building, bidirectional best hits and
one-to-a-genome distribution, to represent a conserved
family.
Length = 188
Score = 29.7 bits (67), Expect = 4.0
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 375 LDSLAHGVAEIEAGDMRDELDDGAYNPLWTMRGFTQTFHFWKESKRAQDW 424
+D+L E++ D+ DELDD A+N L FTQ H W + + Q W
Sbjct: 66 IDALRAKGREVKVSDLDDELDDEAFNAL-----FTQNGH-WAQHGQPQHW 109
>gnl|CDD|214356 CHL00078, rpl5, ribosomal protein L5.
Length = 181
Score = 28.7 bits (65), Expect = 8.0
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 6 VSNLEKSFVLSGILQ-NKVKKIIVNIGEDESILKSTTTLEQLLEEIN 51
V L + F+ I Q K+KKI++N G E+ +++ LE ++E+
Sbjct: 14 VPKLIEKFLYKNIHQVPKLKKIVINRGLGEA-SQNSKILESSIKELT 59
>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 = 28.7 bits (65), Expect = 10.0
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 533 VRVDLNVLNYDGNLLGCCSIAALAAL 558
+ V L VL DG+LL C AA AL
Sbjct: 89 ISVVLQVLQDDGSLLACAINAACLAL 114
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
0.316 0.132 0.391
Gapped
Lambda K H
0.267 0.0595 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 38,098,089
Number of extensions: 3712604
Number of successful extensions: 3063
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3054
Number of HSP's successfully gapped: 24
Length of query: 756
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 652
Effective length of database: 6,324,786
Effective search space: 4123760472
Effective search space used: 4123760472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.3 bits)