RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4496
(228 letters)
>gnl|CDD|216523 pfam01480, PWI, PWI domain.
Length = 74
Score = 61.5 bits (150), Expect = 8e-13
Identities = 16/39 (41%), Positives = 28/39 (71%)
Query: 25 LDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKVSTI 63
L+++KPWI +K+T++LG EDD+V+ ++ N LE +
Sbjct: 1 LEVIKPWIEKKVTEILGFEDDIVIDYILNLLEDKHNPDP 39
>gnl|CDD|214609 smart00311, PWI, PWI, domain in splicing factors.
Length = 74
Score = 53.5 bits (129), Expect = 6e-10
Identities = 18/41 (43%), Positives = 30/41 (73%)
Query: 20 MTKVKLDILKPWITQKITQLLGMEDDVVVAFVYNQLEAEKV 60
++K+KLD +KPWIT+K+ + LG E+D +V F+ +Q+ K
Sbjct: 1 LSKLKLDEIKPWITKKVIEFLGFEEDTLVEFILSQIRQHKG 41
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of the
ribosome. The stalk base consists of a portion of the
23S rRNA and ribosomal proteins L11 and L10. An extended
C-terminal helix of L10 provides the binding site for
L7/L12. L7/L12 consists of two domains joined by a
flexible hinge, with the helical N-terminal domain (NTD)
forming pairs of homodimers that bind to the extended
helix of L10. It is the only multimeric ribosomal
component, with either four or six copies per ribosome
that occur as two or three dimers bound to the L10
helix. L7/L12 is the only ribosomal protein that does
not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They are
exposed to the cytoplasm and contain binding sites for
other molecules. Initiation factors, elongation factors,
and release factors are known to interact with the
L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
has minimal effect on factor binding and it has been
proposed that L7/L12 induces the catalytically active
conformation of EF-Tu and EF-G, thereby stimulating the
GTPase activity of both factors. In eukaryotes, the
proteins that perform the equivalent function to L7/L12
are called P1 and P2, which do not share sequence
similarity with L7/L12. However, a bacterial L7/L12
homolog is found in some eukaryotes, in mitochondria and
chloroplasts. In archaea, the protein equivalent to
L7/L12 is called aL12 or L12p, but it is closer in
sequence to P1 and P2 than to L7/L12.
Length = 127
Score = 46.4 bits (111), Expect = 9e-07
Identities = 12/45 (26%), Positives = 22/45 (48%)
Query: 161 PKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
K+ ++ + LTLLE A+L L+++ + + A A A
Sbjct: 1 LKVEEIVEALKELTLLEAAELVKALEEKFGVSASAAAAAAAAAAP 45
>gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein MauD.
This protein, MauD, appears critical to proper formation
of the small subunit of methylamine dehydrogenase, which
has both an unusual tryptophan tryptophylquinone
cofactor and multiple disulfide bonds. MauD shares
sequence similarity, including a CPxC motif, with a
number of thiol:disulfide interchange proteins. In MauD
mutants, the small subunit apparently does not form
properly and is rapidly degraded [Protein fate, Protein
folding and stabilization, Energy metabolism, Amino
acids and amines].
Length = 189
Score = 29.4 bits (66), Expect = 1.2
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 189 LNLPD---APMMAMGAFAQGRYLRTIFDATSCEI--KLFPSI 225
NLPD P+ G+ A GR +F A SC + KLFP I
Sbjct: 55 FNLPDFDGEPVRIGGSIAPGRPTLLMFTAPSCPVCDKLFPII 96
>gnl|CDD|223300 COG0222, RplL, Ribosomal protein L7/L12 [Translation, ribosomal
structure and biogenesis].
Length = 124
Score = 28.0 bits (63), Expect = 2.0
Identities = 9/46 (19%), Positives = 21/46 (45%)
Query: 160 SPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
+ ++ + LT+LE ++L L+++ + A +A A
Sbjct: 2 ALTKEQIIEALKELTVLELSELVKALEEKFGVTAAAPVAAAAAGAA 47
>gnl|CDD|219597 pfam07823, CPDase, Cyclic phosphodiesterase-like protein. Cyclic
phosphodiesterase (CPDase) is involved in the tRNA
splicing pathway. This protein exhibits a bilobal
arrangement of two alpha-beta modules. Two antiparallel
helices are found on the outer side of each lobe and
frame an antiparallel beta-sheet that is wrapped around
an accessible cleft. Moreover, the beta-strands of each
lobe interact with the other lobe. The central
water-filled cavity houses the enzyme's active site.
Length = 192
Score = 28.1 bits (63), Expect = 2.9
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 112 TITRTYYSKIYLTCKPTK--VSAQTATEAVSSSSEQPFPIPTPDGADKT---YSPKITKL 166
+ +Y+ K+YL +PT +S E IP + T Y P ++ L
Sbjct: 80 SSGDSYFQKVYLEVEPTPELLSLADII------RELFVEIPPQRADEWTSEEYHPHLSLL 133
Query: 167 ANDIS 171
D+S
Sbjct: 134 YGDLS 138
>gnl|CDD|214358 CHL00083, rpl12, ribosomal protein L12.
Length = 131
Score = 27.2 bits (61), Expect = 3.6
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 160 SPKITKLANDISSLTLLECADLSSLLKKQLNLPD---APMMAMGAFA 203
S KI ++ ++ SLTLLE A+L +++ + M A A
Sbjct: 2 STKINEIIEELKSLTLLEAAELVKQIEETFGVDASAPVGGGMMSAPA 48
>gnl|CDD|234671 PRK00157, rplL, 50S ribosomal protein L7/L12; Reviewed.
Length = 123
Score = 27.1 bits (61), Expect = 3.7
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 162 KITK--LANDISSLTLLECADLSSLLKKQLNLPDAPMMAMGAFAQG 205
+TK + + +T+LE ++L L+++ + A +A A A
Sbjct: 2 ALTKEQIIEALKEMTVLELSELVKALEEKFGVSAAAPVAAAAAAAA 47
>gnl|CDD|131133 TIGR02078, AspKin_pair, Pyrococcus aspartate kinase subunit,
putative. This family consists of proteins restricted
to and found as paralogous pairs (typically close
together) in species of Pyrococcus, a hyperthermophilic
archaeal genus. Members are always found close to other
genes of threonine biosynthesis and appear to represent
the Pyrococcal form of aspartate kinase. Alignment to
aspartokinase III from E. coli shows that 300 N-terminal
and 20 C-terminal amino acids are homologous, but the
form in Pyrococcus lacks ~ 100 amino acids in between
[Amino acid biosynthesis, Aspartate family].
Length = 327
Score = 27.8 bits (62), Expect = 4.7
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 153 DGADKTYSPKITKLANDISSLTLLECADLSSLLKKQLNLPDAPMMAM 199
+ DK+ + +I ++ + + ++ LS LK+ N PD P A+
Sbjct: 50 NTFDKSAALEIEEIYEEFAKELGVDLNILSPYLKELFNPPDLPKEAL 96
>gnl|CDD|218171 pfam04608, PgpA, Phosphatidylglycerophosphatase A. This family
represents a family of bacterial
phosphatidylglycerophosphatases (EC:3.1.3.27), known as
PgpA. It appears that bacteria possess several
phosphatidylglycerophosphatases, and thus, PgpA is not
essential in Escherichia coli.
Length = 144
Score = 26.7 bits (60), Expect = 6.3
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 25 LDILKPWITQKITQLLG-----MEDDVVVAF 50
DI+KP + + + M DD++
Sbjct: 104 FDIVKPGPIGWLDRRVKGGLGVMLDDILAGI 134
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional.
Length = 1195
Score = 27.6 bits (61), Expect = 6.5
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 105 KILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIPTPDGADK 157
K+ G +TI + S + + KP+K A A ++S + P+ TP
Sbjct: 972 KLFSGGQTIIMRFPSSVKAS-KPSKFEATPAKGPLTSGKQSTLPMATPAQPPV 1023
>gnl|CDD|215481 PLN02889, PLN02889, oxo-acid-lyase/anthranilate synthase.
Length = 918
Score = 27.5 bits (61), Expect = 8.0
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 104 RKILRGRKTITRTYYSKIYLTCKPTKVSAQTATEAVSSSSEQPFPIP----TPDGADKTY 159
R+I + + IT+ Y+ ++ T + S TA V +S Q F +P +G D
Sbjct: 325 RQIFKNFREITQDYWLRLRSTSLRRRNSNLTANMQVPDAS-QLFKVPRRGQLGNGEDALG 383
Query: 160 SPKITKLANDISSLTLLECADLS 182
+ ++++ A S+ + +LS
Sbjct: 384 NRELSRRAQLRGSVDVFSLLNLS 406
>gnl|CDD|222429 pfam13873, Myb_DNA-bind_5, Myb/SANT-like DNA-binding domain. This
presumed domain appears to be related to other Myb/SANT
like DNA binding domains. This family is greatly
expanded in arthropods and higher eukaryotes.
Length = 78
Score = 25.7 bits (57), Expect = 8.1
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 93 LAILMQEVEGRRKILRGRKTITRT 116
L +L++ VE + IL G+K+ T
Sbjct: 10 LLVLVELVEKHKDILEGKKSDAAT 33
>gnl|CDD|224249 COG1330, RecC, Exonuclease V gamma subunit [DNA replication,
recombination, and repair].
Length = 1078
Score = 27.3 bits (61), Expect = 8.1
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 5 VFALTSKPQVVQKVDMTKVKLDILKPWIT 33
V L P + + +T+ +L L+ W+
Sbjct: 437 VLDLLDVPPLAARFGITEEELLTLRHWVE 465
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like
subfamily of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Neisseria
meningitides Nape and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different AP
endonuclease enzymes catalyze the different reactions
with different efficiences. Many organisms have two AP
endonucleases, usually one is the dominant AP
endonuclease, the other has weak AP endonuclease
activity; for example, Neisseria meningitides Nape and
NExo. Nape, found in this subfamily, is the dominant AP
endonuclease. It exhibits strong AP endonuclease
activity, and also exhibits 3'-5'exonuclease and
3'-deoxyribose phosphodiesterase activities.
Length = 253
Score = 26.8 bits (60), Expect = 9.3
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 192 PDAPMMAMG---AFAQGRYLRTIFDATSCEIKLFPS 224
P A + +G +GRY+ FD S PS
Sbjct: 76 PKAVIYGLGFEEFDDEGRYIEADFDNVSVASLYVPS 111
>gnl|CDD|133477 cd06971, PgpA, Phosphatidylglycerophosphatase A; a bacterial
membrane-associated enzyme involved in lipid metabolism.
Phosphatidylglycerophosphatase A domain represents a
family of bacterial membrane-associated enzymes involved
in lipid metabolism. The prototype of this CD is a
putative Phosphatidylglycerophosphatase A (PGPase A)
from Listeria monocytogenes. PGPase A (EC: 3.1.3.27),
encoded by the gene pgpA, specifically catalyzes the
formation of phosphatidylglycerol from phosphatidyl
glycerophosphate (PGP). It requires Mg2+ for activity
and is inhibited by sulfhydryl agents and
freezing/thawing. PGPase B encoded from pgpB is not
included in this family, which also acts on phosphatidic
acid (PA) and lysophosphatidic acid (LPA). Aside from
PGPase A and B, evidence shows that there is another
PGPase existing in E. coli. Thus, PGPase A is not
essential for PGPase activity in E. coli.
Length = 143
Score = 26.3 bits (59), Expect = 9.9
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 25 LDILKPWITQKITQLLG-----MEDDVVVAFV 51
DI+KP + + + M DD++
Sbjct: 103 FDIVKPGPIGWLDRKVKGGLGVMLDDILAGLY 134
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 0.133 0.378
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,160,208
Number of extensions: 1006963
Number of successful extensions: 824
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 22
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
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: 57 (25.8 bits)