RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13090
(771 letters)
>gnl|CDD|133160 cd06096, Plasmepsin_5, Plasmepsins are a class of aspartic
proteinases produced by the plasmodium parasite. The
family contains a group of aspartic proteinases
homologous to plasmepsin 5. Plasmepsins are a class of
at least 10 enzymes produced by the plasmodium parasite.
Through their haemoglobin-degrading activity, they are
an important cause of symptoms in malaria sufferers.
This family of enzymes is a potential target for
anti-malarial drugs. Plasmepsins are aspartic acid
proteases, which means their active site contains two
aspartic acid residues. These two aspartic acid residue
act respectively as proton donor and proton acceptor,
catalyzing the hydrolysis of peptide bond in proteins.
Aspartic proteinases are composed of two structurally
similar beta barrel lobes, each lobe contributing an
aspartic acid residue to form a catalytic dyad that acts
to cleave the substrate peptide bond. The catalytic Asp
residues are contained in an Asp-Thr-Gly-Ser/thr motif
in both N- and C-terminal lobes of the enzyme. There
are four types of plasmepsins, closely related but
varying in the specificity of cleavage site. The name
plasmepsin may come from plasmodium (the organism) and
pepsin (a common aspartic acid protease with similar
molecular structure). This family of aspartate proteases
is classified by MEROPS as the peptidase family A1
(pepsin A, clan AA).
Length = 326
Score = 34.3 bits (79), Expect = 0.21
Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 235 ISFTCDECHLC----FNTFRRFDSHIRAHEYTEQCELCNEKVIGKNQ-IYFHYYHE 285
+SF C +C C + +S + Y + + C N+ Y Y E
Sbjct: 28 LSFPCSQCKNCGIHMEPPYNLNNSITSSILYCDCNKCCYCLSCLNNKCEYSISYSE 83
>gnl|CDD|165245 PHA02934, PHA02934, Hypothetical protein; Provisional.
Length = 253
Score = 32.3 bits (73), Expect = 0.86
Identities = 17/36 (47%), Positives = 22/36 (61%)
Query: 103 DDDDDDDDGDDGDVKFDVCNGIINKIENTCSEHNDR 138
DD DD DD DD D D+ NGI+ IE+ S ++D
Sbjct: 28 DDIDDIDDIDDIDNVQDIDNGIVQDIEDEASNNDDH 63
>gnl|CDD|151714 pfam11273, DUF3073, Protein of unknown function (DUF3073). This
family of proteins with unknown function appears to be
restricted to Actinobacteria.
Length = 64
Score = 29.2 bits (66), Expect = 1.1
Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 77 LKYH---MHVDMLQY-LYGASFDRFPHLSNDDDDDDDDGDD 113
LKY +D LQ L G S + +DD DD D
Sbjct: 16 LKYSSPDTDLDALQRELSGGSSRSSADDDDQYEDDYDDYDK 56
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 27.9 bits (63), Expect = 1.2
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 630 QLTCDICDRVFQTDKQWKLHM 650
Q C CD+ F+++ + H+
Sbjct: 1 QFYCVACDKYFKSENALENHL 21
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 32.1 bits (73), Expect = 1.4
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 572 KHQCPVCLRRFSRQSDNNTHQRRVHGV 598
+ C VC+ FS HQR H +
Sbjct: 73 SYVCNVCMAEFSSMDQLAEHQRTTHSI 99
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 27.7 bits (62), Expect = 1.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 48 NMKNHIMTHTGSKPYNCSHCTFK 70
N++ H+ THTG KPY C C
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKS 23
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 30.0 bits (67), Expect = 5.9
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 5/37 (13%)
Query: 542 GEKYSCTQCSYQTYHKHALDNHMPLHSLDRKHQCPVC 578
++ C ++ +H +D + L ++CPVC
Sbjct: 336 NDRLRVLPCDHR-FHVGCVDKWL----LGYSNKCPVC 367
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 29.6 bits (67), Expect = 6.2
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 325 SASKKSVLLSHLKQHVTRVTRTQHMTPDE------ETNEIPIEPD 363
A++ +LL H ++H+ + + M P E E + I I PD
Sbjct: 46 LATEDELLLCHSEEHLDEMKSLEKMKPRELNRLGKEYDSIYIHPD 90
>gnl|CDD|177868 PLN02222, PLN02222, phosphoinositide phospholipase C 2.
Length = 581
Score = 29.6 bits (66), Expect = 6.6
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 100 LSNDDDDDDDDGDD 113
+ DDDDDDDDG+D
Sbjct: 293 SNGDDDDDDDDGED 306
>gnl|CDD|215555 PLN03063, PLN03063, alpha,alpha-trehalose-phosphate synthase
(UDP-forming); Provisional.
Length = 797
Score = 29.8 bits (67), Expect = 7.6
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 298 FTTKTPKKFIEHKEAGHFTWNCEHCD--FSASKKSVLLSHL 336
FT +TP+ ++E E WN E+ D F ++ +L HL
Sbjct: 612 FTDRTPRSYVEKSETS-LVWNYEYADVEFGRAQARDMLQHL 651
>gnl|CDD|114308 pfam05578, Peptidase_S31, Pestivirus NS3 polyprotein peptidase S31.
These serine peptidases are involved in processing of
the flavivirus polyprotein.
Length = 211
Score = 28.9 bits (64), Expect = 7.8
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 158 KMTRESGIKLNIKYDMNEAEDLKCKLCNYQAVNIKGIRAHVFRKHLQNT 206
K+T E+ + +K D + +C + N +AVNI G + V HLQ T
Sbjct: 94 KLTDET--EYGVKTDSGCPDGARCYVLNPEAVNISGSKGAVV--HLQKT 138
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 27.6 bits (62), Expect = 7.8
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 479 CYLCEEKFENSESLRTHMNS 498
C C ++F++ E+LR HM
Sbjct: 53 CLYCGKQFKSLEALRQHMRD 72
>gnl|CDD|165163 PHA02811, PHA02811, putative host range protein; Provisional.
Length = 197
Score = 28.9 bits (64), Expect = 8.3
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 77 LKYHMHVDMLQYLYGASFDRFPHLSNDDDDDDDDGDDGDVKFDVCNGIINKIE 129
LK ++++ YLY A +S+DDDDD+D+ D+ D + D N I + E
Sbjct: 148 LKDYINISDDYYLYDACDYCI--ISSDDDDDNDNADN-DEEDDEVNDIEDDYE 197
>gnl|CDD|172940 PRK14465, PRK14465, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 342
Score = 29.2 bits (65), Expect = 8.9
Identities = 29/134 (21%), Positives = 51/134 (38%), Gaps = 32/134 (23%)
Query: 242 CHLCFNTFRRFDSHIRAHEYTEQCELCNEKVIGKNQI-------------YF------HY 282
C C F +++AHE +Q L EK++G YF
Sbjct: 119 CKFCATAKLEFQGNLKAHEIVDQV-LQVEKIVGDRATNVVFMGMGEPMHNYFNVIRAASI 177
Query: 283 YHEHEGYDFNCKQCSFTTKTP----KKFIEHKEAGHFTWNCEHCDFSASKKSVL------ 332
H+ + ++ K+ + +T ++FIE+KE +F + H D + + ++
Sbjct: 178 LHDPDAFNLGAKRITISTSGVVNGIRRFIENKEPYNFAISLNHPDPNG-RLQIMDIEEKF 236
Query: 333 -LSHLKQHVTRVTR 345
L L Q TR
Sbjct: 237 PLEELLQAAKDFTR 250
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 29.1 bits (65), Expect = 10.0
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 155 PKYKMTRESGIKLNIKYDMNEAEDLKCKLCNYQAVNIKGI 194
P YK++++ G K+ + E E +K KL NY KG+
Sbjct: 534 PLYKLSKKDGKKVKYAWSDLELESVKKKLKNYTLQRYKGL 573
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
0.323 0.134 0.432
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,445,531
Number of extensions: 3337206
Number of successful extensions: 3641
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3620
Number of HSP's successfully gapped: 77
Length of query: 771
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 667
Effective length of database: 6,324,786
Effective search space: 4218632262
Effective search space used: 4218632262
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 63 (28.0 bits)