RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6037
(286 letters)
>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease. The major pathways of
mRNA turnover in eukaryotes initiate with shortening of
the polyA tail. CAF1 encodes a critical component of the
major cytoplasmic deadenylase in yeast. Both Caf1p is
required for normal mRNA deadenylation in vivo and
localises to the cytoplasm. Caf1p copurifies with a
Ccr4p-dependent polyA-specific exonuclease activity.
Some members of this family include and inserted RNA
binding domain pfam01424. This family of proteins is
related to other exonucleases pfam00929 (Bateman A pers.
obs.). The crystal structure of Saccharomyces cerevisiae
Pop2 has been resolved at 2.3 Angstrom#resolution.
Length = 235
Score = 300 bits (771), Expect = e-103
Identities = 131/237 (55%), Positives = 158/237 (66%), Gaps = 9/237 (3%)
Query: 15 REVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDLL 74
REVW N EEF IR I++Y++I IDTEFPGVVA+P+G FRSTS+Y+Y L+ NVD L
Sbjct: 1 REVWRSNFHEEFKEIRQAIDSYDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRL 60
Query: 75 KIIQIGLTFFDSKSCTPPGPFTTWQFNFK-FDLQEDMYAQDSIDLLQNSGIQFQRHKEEG 133
KIIQ+GLT FD K P + TWQFNF F+L+ED YA SI+ L G F +H+ EG
Sbjct: 61 KIIQLGLTLFDEKGNLPDSYY-TWQFNFSLFNLEEDFYAPSSIEFLAKQGFDFNKHRREG 119
Query: 134 IEPADFAELLTTSGVVLND-KVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLF 192
I FAELL +SG+ LN V W++FH YDFGYLLKLL G LP +F EL R
Sbjct: 120 IPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTG-GPLPETLDDFLELLREL 178
Query: 193 FKSIYDVKYLMKSCKNLKG----GLQEVAEQLDLSR-IGPQHQAGSDSLLTGRVFFK 244
F +YD KYL K C L G GLQE+A+ L ++R +G HQAGSDSLLT VFFK
Sbjct: 179 FPRVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFFK 235
>gnl|CDD|227553 COG5228, POP2, mRNA deadenylase subunit [RNA processing and
modification].
Length = 299
Score = 301 bits (772), Expect = e-102
Identities = 122/266 (45%), Positives = 171/266 (64%), Gaps = 3/266 (1%)
Query: 14 IREVWARNVQEEFVHIRSLINTYNYIGIDTEFPGVVAKPLGDFRSTSEYQYHFLKINVDL 73
IR+VW N+ E IR LI+ YN++ +DTEFPGVVA+P+G F+S+ +Y Y L+ NVD
Sbjct: 20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDF 79
Query: 74 LKIIQIGLTFFDSKSCTPPGPFTTWQFNFKFDLQEDMYAQDSIDLLQNSGIQFQRHKEEG 133
LKIIQ+GL+ D P GP +TWQFNF+FDL++DMYA +SI+LL+ SGI F++H+ G
Sbjct: 80 LKIIQLGLSLSDENGNKPNGP-STWQFNFEFDLKKDMYATESIELLRKSGIDFKKHENLG 138
Query: 134 IEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKLLMGTRSLPSEEAEFFELQRLFF 193
I+ +F+ELL SG+V+++ V W++FHS YDFGYL+K+L LP+ + +F+ +F
Sbjct: 139 IDVFEFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILT-NDPLPNNKEDFYWWLHQYF 197
Query: 194 KSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDA 253
+ YD+K + KS N GLQE+ L L R G QHQAGSD+LLT FF R F +
Sbjct: 198 PNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTS 257
Query: 254 IDDDKYCGHIYGLGPAGWNGHTNGNA 279
I + G + + H N
Sbjct: 258 IGQSLLM-LLSGCQLSKLSLHKFPNG 282
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 31.5 bits (72), Expect = 0.28
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 212 GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFF 250
L+++A++L L I H+A D+ T ++F K+ E
Sbjct: 131 SLKKLAKRLLLEVIQRAHRALDDARATAKLFKKLLERLE 169
>gnl|CDD|163212 TIGR03307, PhnP, phosphonate metabolism protein PhnP. This family
of proteins found in operons encoding phosphonate C-P
lyase systems as is observed in E. coli and is a member
of the metallo-beta-lactamase superfamily (pfam00753).
As defined by this model, all instances of this protein
are associated with the C-P lyase, but not all genomes
containing the C-P lyase system contain phnP.
Length = 238
Score = 31.2 bits (71), Expect = 0.48
Identities = 24/82 (29%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLK------ 170
DL ++ GI E EP D L T + L HS FGYLL+
Sbjct: 97 DLFKHPGILDFSKPLEAFEPFDLGGLRVTP-LPLV--------HSKLTFGYLLETDGQRV 147
Query: 171 -LLMGTRSLPSEEAEFFELQRL 191
L T LP + F + L
Sbjct: 148 AYLTDTAGLPPDTEAFLKNHPL 169
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 31.5 bits (72), Expect = 0.57
Identities = 11/33 (33%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 213 LQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
L++++E+L L P H+A SD+ +T +F ++
Sbjct: 134 LRDLSEELGLEHDQP-HRADSDAEVTAELFLQL 165
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 30.9 bits (70), Expect = 0.84
Identities = 13/32 (40%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 29 IRSLINTYNY--IGIDTEFPGVVAKPLGDFRS 58
I+ L++ YN+ IG DT+ G++ KP+G +S
Sbjct: 236 IKDLLDLYNFRQIGPDTKVYGIIGKPVGHSKS 267
>gnl|CDD|183052 PRK11244, phnP, carbon-phosphorus lyase complex accessory protein;
Provisional.
Length = 250
Score = 29.2 bits (66), Expect = 2.2
Identities = 25/83 (30%), Positives = 32/83 (38%), Gaps = 16/83 (19%)
Query: 117 DLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSGYDFGYLLKL----- 171
DL ++ GI H E EP D L T + LN HS FGYLL+
Sbjct: 107 DLFKHPGILDFSHPLEPFEPFDLGGLQVTP-LPLN--------HSKLTFGYLLETAHSRV 157
Query: 172 --LMGTRSLPSEEAEFFELQRLF 192
L T LP + +F +
Sbjct: 158 AYLTDTVGLPEDTLKFLRNNQPD 180
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 29.3 bits (66), Expect = 3.2
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 212 GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKMRELFFEDAI 254
L + ++L + + H+A D+ T +VF M E E I
Sbjct: 319 RLGNICKKLGVD-LDDHHRADYDAEATAKVFKVMVEQLKEKGI 360
>gnl|CDD|171490 PRK12425, PRK12425, fumarate hydratase; Provisional.
Length = 464
Score = 28.7 bits (64), Expect = 3.9
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 115 SIDLLQNSGIQFQRHKEEGIEP--ADFAELLTTSGVVLNDKVKWLSFHSGYD 164
SI LL + FQ+H G+EP A L G++L V L+ H GYD
Sbjct: 370 SIRLLADGCRNFQQHCVAGLEPDAEQMAAHL-ERGLML---VTALNPHIGYD 417
>gnl|CDD|99836 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of
Caenorhabditis elegans ERI-1, human 3' exonuclease, and
similar proteins. This subfamily is composed of
Caenorhabditis elegans ERI-1, human 3' exonuclease
(3'hExo), Drosophila exonuclease snipper (snp), and
similar proteins from eukaryotes and bacteria. These are
DEDDh-type DnaQ-like 3'-5' exonucleases containing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific Hx(4)D conserved pattern at ExoIII.
These motifs are clustered around the active site and
contain four conserved acidic residues that serve as
ligands for the two metal ions required for catalysis.
ERI-1 has been implicated in the degradation of small
interfering RNAs (RNAi). 3'hExo participates in the
degradation of histone mRNAs. Snp is a non-essential
exonuclease that efficiently degrades structured RNA and
DNA substrates as long as there is a minimum of 2
nucleotides in the 3' overhang to initiate degradation.
Snp is not a functional homolog of either ERI-1 or
3'hExo.
Length = 176
Score = 28.0 bits (63), Expect = 4.8
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 192 FFKSIYDVKYLMKSCKNLKG--GLQEVAEQLDLSRIGPQHQAGSDSLLTGRVFFKM 245
FF+ D+K LK GL + E L L G H+ D+ R+ ++
Sbjct: 120 FFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175
>gnl|CDD|222337 pfam13714, PEP_mutase, Phosphoenolpyruvate phosphomutase. This
domain includes the enzyme Phosphoenolpyruvate
phosphomutase (EC:5.4.2.9). The PEP mutase from
Streptomyces viridochromogenes has been characterized as
catalyzing the formation of a carbon-phosphorus bond by
converting phosphoenolpyruvate (PEP) to
phosphonopyruvate (P-Pyr). This enzyme has a TIM barrel
fold.
Length = 238
Score = 27.5 bits (62), Expect = 7.6
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 210 KGGLQEVAEQLDLSRIGPQHQAGSDSLLTGR--VFFKMRELFFEDAID 255
GGL ++ E R + ++ R F E+AI+
Sbjct: 112 GGGLYDIEEFAAKIRAARAAAEDAGFVINARTDAFLLGAGDGLEEAIE 159
>gnl|CDD|220373 pfam09738, DUF2051, Double stranded RNA binding protein (DUF2051).
This is a novel protein identified as interacting with
the leucine-rich repeat domain of human flightless-I,
FliI protein.
Length = 294
Score = 27.6 bits (61), Expect = 8.3
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 177 SLPSEEAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQL 220
L E ELQR F + D++ L ++ L+ L+E+ EQL
Sbjct: 119 KLEELEESLAELQREFEEKTRDLEALKRAIDILQHQLKELKEQL 162
>gnl|CDD|217583 pfam03473, MOSC, MOSC domain. The MOSC (MOCO sulfurase C-terminal)
domain is a superfamily of beta-strand-rich domains
identified in the molybdenum cofactor sulfurase and
several other proteins from both prokaryotes and
eukaryotes. These MOSC domains contain an absolutely
conserved cysteine and occur either as stand-alone
forms, or fused to other domains such as NifS-like
catalytic domain in Molybdenum cofactor sulfurase. The
MOSC domain is predicted to be a sulfur-carrier domain
that receives sulfur abstracted by the pyridoxal
phosphate-dependent NifS-like enzymes, on its conserved
cysteine, and delivers it for the formation of diverse
sulfur-metal clusters.
Length = 124
Score = 26.6 bits (59), Expect = 8.5
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 111 YAQDSIDLLQNSGIQFQRHKEEGIEPADFAELLTTSGVVLNDKVKWLSFHSG 162
+++S+ L R ++P F E L SG+ + G
Sbjct: 24 ISRESLADLN------ARLGLRLLDPGRFRENLVVSGLEEDTWCIGDRIRIG 69
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 27.8 bits (63), Expect = 9.1
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 10/30 (33%)
Query: 228 QHQAGSDSLLTGRVFFKM---RELFFEDAI 254
Q+ D+LL FF+M ELFFEDA
Sbjct: 21 QYP---DALL----FFRMGDFYELFFEDAK 43
>gnl|CDD|227351 COG5018, KapD, Inhibitor of the KinA pathway to sporulation,
predicted exonuclease [General function prediction
only].
Length = 210
Score = 27.2 bits (60), Expect = 9.5
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 9/64 (14%)
Query: 182 EAEFFELQRLFFKSIYDVKYLMKSCKNLKGGLQEVAEQLDLSRIGPQHQAGSDSLLTGRV 241
+ +L L +K+++ L GL + E+ S G H+A D+ R+
Sbjct: 127 KGPMVDL-SLEYKNVFGDPRLT--------GLNKALEEYGDSFTGTHHRALDDARNAYRL 177
Query: 242 FFKM 245
F +
Sbjct: 178 FKLV 181
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
0.320 0.139 0.420
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,920,020
Number of extensions: 1433743
Number of successful extensions: 1082
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1074
Number of HSP's successfully gapped: 22
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
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)