RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6392
(198 letters)
>gnl|CDD|211907 TIGR04184, ATPgraspMvdD, ATP-grasp ribosomal peptide maturase, MvdD
family. The pair of ATP-grasp proteins MvdD and MvdC
(microviridin D and C), as well as an acetyltransferase,
produce microviridin K, an example of a RiPP
(ribosomally synthesized and posttranslationally
modified peptide). Microviridins are peptidase
inhibitors.
Length = 321
Score = 32.8 bits (75), Expect = 0.089
Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 19/94 (20%)
Query: 91 VIAAIERNGEAIPLRFQP---PQDAIL--YYSNPESRGYLADPEQ------IS--WQRFA 137
V AIE G RF P + L YY + + +L +Q +S W R
Sbjct: 16 VTKAIEAQGGKA-FRFDTDRYPTEVQLDIYYGDGTEQSFLTTEDQKLDLSDVSAVWYRRM 74
Query: 138 LAQKYGYTLPEIEKDPDFEMLSMRKDPRQVFYGL 171
+ G LP+ E D S+ ++ R G+
Sbjct: 75 ---RIGKKLPD-EMDKQLREASV-EESRATIRGM 103
>gnl|CDD|202007 pfam01846, FF, FF domain. This domain has been predicted to be
involved in protein-protein interaction. This domain was
recently shown to bind the hyperphosphorylated
C-terminal repeat domain of RNA polymerase II,
confirming its role in protein-protein interactions.
Length = 50
Score = 26.3 bits (59), Expect = 2.0
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 145 TLPEIEKDPDFEMLSMRKDPRQVF 168
++EKDP ++ L + Q+F
Sbjct: 24 IKKKLEKDPRYKALLSPSEREQLF 47
>gnl|CDD|199903 cd10150, CobN_like, CobN subunit of cobaltochelatase, bchH and chlH
subunits of magnesium chelatases, and similar proteins.
Cobaltochelatase is a complex enzyme that catalyzes the
insertion of cobalt into hydrogenobyrinic acid
a,c-diamide, resulting in cobyrinic acid, as
demonstrated for Pseudomonas denitrificans. This is an
essential step in the bacterial synthesis of cobalamine
(B12). The insertion of cobalt requires a complex
composed of three polypeptides, cobN, cobS, and cobT.
Also included in this family are protoporphyrin IX
magnesium chelatases involved in the synthesis of
chlorophyll and bacteriochlorophyll, specifically the
large (chlH or bchH) subunits.They are thought to bind
both the protoporphyrin and the magnesium ion.
Hydrolysis of ATP by the smaller subunits in the complex
may trigger a conformational change that results in the
insertion of the ion into the protoporphyrin scaffold.
Cryo electron microscopy studies have suggested that a
distinct bchH C-terminal domain may bind tightly to the
N-terminal domain upon substrate binding, requiring a
substantial conformational change of the bchH subunit.
It has also been suggested that chlH of higher plants
binds abscisic acid via a C-terminal domain and plays a
role in abscisic acid signaling, and that the protein
spans the chloroplast envelope, with the C-terminus
exposed to the cytosol.
Length = 910
Score = 28.7 bits (65), Expect = 2.0
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 104 LRFQPPQD---AILYYSNP--ESR---GYLADPEQISWQRFALAQKYGYTLPEIEKDPD 154
LR +P + AI+ Y+ P + D + GY + E+ + +
Sbjct: 313 LRRKPNAEKKIAIILYNYPPGKGNIGAAVGLDTPSSLSLLLIRLKAEGYGVGELPESGE 371
>gnl|CDD|234263 TIGR03568, NeuC_NnaA, UDP-N-acetyl-D-glucosamine 2-epimerase,
UDP-hydrolysing. This family of enzymes catalyzes the
combined epimerization and UDP-hydrolysis of
UDP-N-acetylglucosamine to N-acetylmannosamine. This is
in contrast to the related enzyme WecB (TIGR00236) which
retains the UDP moiety. NeuC acts in concert with NeuA
and NeuB to synthesize CMP-N5-acetyl-neuraminate.
Length = 365
Score = 28.6 bits (65), Expect = 2.3
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 138 LAQKYGYTLPEIEKD 152
L+ +YG T+ EIEKD
Sbjct: 40 LSPEYGNTVNEIEKD 54
>gnl|CDD|224680 COG1766, fliF, Flagellar basal body M-ring protein [Cell motility
and secretion].
Length = 545
Score = 28.1 bits (63), Expect = 3.2
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 10/47 (21%)
Query: 72 GADNFKAKINIEVQWTSEPVIAAIERNGEAIPLRFQPPQDAILYYSN 118
GA N +A + E+ ++ A E E ++ P S
Sbjct: 259 GAGNVRASVTAELDFS------AKESTEE----KYDPNGREPAVRSE 295
>gnl|CDD|238729 cd01452, VWA_26S_proteasome_subunit, 26S proteasome plays a major
role in eukaryotic protein breakdown, especially for
ubiquitin-tagged proteins. It is an ATP-dependent
protease responsible for the bulk of non-lysosomal
proteolysis in eukaryotes, often using covalent
modification of proteins by ubiquitylation. It consists
of a 20S proteolytic core particle (CP) and a 19S
regulatory particle (RP). The CP is an ATP independent
peptidase consisting of hydrolyzing activities. One or
both ends of CP carry the RP that confers both ubiquitin
and ATP dependence to the 26S proteosome. The RP's
proposed functions include recognition of substrates and
translocation of these to CP for proteolysis. The RP can
dissociate into a stable lid and base subcomplexes. The
base is composed of three non-ATPase subunits (Rpn 1, 2
and 10). A single residue in the vWA domain of Rpn10 has
been implicated to be responsible for stabilizing the
lid-base association.
Length = 187
Score = 27.3 bits (61), Expect = 4.7
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 97 RNGEAIPLRFQPPQDAILYY------SNPES 121
RNG+ P RFQ DA+ SNPE+
Sbjct: 17 RNGDYPPTRFQAQADAVNLICQAKTRSNPEN 47
>gnl|CDD|198017 smart00949, PAZ, This domain is named PAZ after the proteins Piwi
Argonaut and Zwille. This domain is found in two
families of proteins that are involved in
post-transcriptional gene silencing. These are the Piwi
family and the Dicer family, that includes the Carpel
factory protein. The function of the domains is unknown
but has been suggested to mediate complex formation
between proteins of the Piwi and Dicer families by
hetero-dimerisation. The three-dimensional structure of
this domain has been solved. The PAZ domain is composed
of two subdomains. One subdomain is similar to the OB
fold, albeit with a different topology. The OB-fold is
well known as a single-stranded nucleic acid binding
fold. The second subdomain is composed of a beta-hairpin
followed by an alpha-helix. The PAZ domains shows
low-affinity nucleic acid binding and appears to
interact with the 3' ends of single-stranded regions of
RNA in the cleft between the two subdomains. PAZ can
bind the characteristic two-base 3' overhangs of siRNAs,
indicating that although PAZ may not be a primary
nucleic acid binding site in Dicer or RISC, it may
contribute to the specific and productive incorporation
of siRNAs and miRNAs into the RNAi pathway.
Length = 138
Score = 26.5 bits (59), Expect = 5.6
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 111 DAILYYSNPESRGYLADPEQISWQRFA--LAQKYGYTLPEIEKDPDFEML 158
D I + P+S +D +I+ F QKY T+ +DP+ +L
Sbjct: 44 DDIDWNLAPKSTFEKSDGSEIT---FVEYYKQKYNITI----RDPNQPLL 86
>gnl|CDD|218423 pfam05089, NAGLU, Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel
domain. Alpha-N-acetylglucosaminidase, a lysosomal
enzyme required for the stepwise degradation of heparan
sulfate. Mutations on the alpha-N-acetylglucosaminidase
(NAGLU) gene can lead to Mucopolysaccharidosis type IIIB
(MPS IIIB; or Sanfilippo syndrome type B) characterized
by neurological dysfunction but relatively mild somatic
manifestations. The structure shows that the enzyme is
composed of three domains. This central domain has a tim
barrel fold.
Length = 333
Score = 26.8 bits (60), Expect = 6.9
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 110 QDAILY-------YSNPESRGYLADPEQISWQRFALAQKYGYTLPE 148
Q+A+ Y S+ E R + P ++W R + +G LP+
Sbjct: 42 QEAVWYRVLLELGLSDEEIREFFTGPAFLAWWRMGNLEGWGGPLPQ 87
>gnl|CDD|131219 TIGR02164, torA, trimethylamine-N-oxide reductase TorA. This very
narrowly defined family represents TorA, part of a
family of related molybdoenzymes that include biotin
sulfoxide reductases, dimethyl sulfoxide reductases, and
at least two different subfamilies of
trimethylamine-N-oxide reductases. A single enzyme from
the larger family may have more than one activity. TorA
typically is located in the periplasm, has a Tat
(twin-arginine translocation)-dependent signal sequence,
and is encoded in a torCAD operon.
Length = 822
Score = 26.7 bits (59), Expect = 9.1
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 59 PFHNHYGVNLTDEGADNFKAKINIEVQWTSEPVIAAIERNGEAIPLRFQPPQDAILYYSN 118
P+H+H N + + + I+V WT+ + I +P Q ++ I Y +
Sbjct: 475 PWHHHQDRNRMKQAFQKLETVVTIDVSWTATCRFSDI-----VLPACTQFERNDIDVYGS 529
Query: 119 PESRGYLA 126
+RG +A
Sbjct: 530 YSNRGIIA 537
>gnl|CDD|215762 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal domain.
This family includes small ribosomal subunit S9 from
prokaryotes and S16 from metazoans. This domain is
predicted to bind to ribosomal RNA. This domain is
composed of four helices in the known structure. However
the domain is discontinuous in sequence and the
alignment for this family contains only the first three
helices.
Length = 93
Score = 25.4 bits (56), Expect = 9.3
Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 14/55 (25%)
Query: 118 NPESRGYLADPEQISW-QRFALAQKYGYTLPEIEKDPDFEMLSMRKDPRQVFYGL 171
+ Y P Q W + +Y L E K + FYGL
Sbjct: 24 TKLAGEYGLRPGQHGWRVKKGRLSRYLLRLDE-------------KQKLRFFYGL 65
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 0.139 0.426
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,967,496
Number of extensions: 1046050
Number of successful extensions: 913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 16
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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 (21.7 bits)
S2: 56 (25.3 bits)