RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|255764504|ref|YP_003064930.2| DNA-methyltransferase MKpn2kI
[Candidatus Liberibacter asiaticus str. psy62]
(101 letters)
>gnl|CDD|143915 pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.
Length = 319
Score = 83.9 bits (208), Expect = 8e-18
Identities = 36/108 (33%), Positives = 52/108 (48%), Gaps = 10/108 (9%)
Query: 1 MKACDFGVPQRRERLYIIDFLNPSV------EFKFPTPLGIKPRLGDILEE--HIDDKST 52
+ A D+GVPQ RER++I+ N + EF FP P + D+LEE ++K
Sbjct: 141 LNASDYGVPQNRERVFIVGIRNDLILNFPVPEFDFPKPSTATDTIRDLLEEPSLDENKYN 200
Query: 53 ISNKLWEGHQKRKENNKIAGKGFGYGLFF--ENSATTNTLSARYYKDG 98
+S+K E H++RK K G G+ Y L + S Y K G
Sbjct: 201 LSDKFVENHERRKPTTKAPGGGYPYLLRNRIDKVEEGKGPSFTYRKSG 248
>gnl|CDD|30619 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 49.7 bits (118), Expect = 2e-07
Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 1/100 (1%)
Query: 3 ACDFGVPQRRERLYIIDFLNPSVEFKFPTPLGIK-PRLGDILEEHIDDKSTISNKLWEGH 61
A D+GVPQ RER++I+ F +++ + R + E ++ +++L+
Sbjct: 149 AADYGVPQSRERVFIVGFRRDNIDLDPNVLPPLPLGRKKTLKEALKNNDLPETDELYLSR 208
Query: 62 QKRKENNKIAGKGFGYGLFFENSATTNTLSARYYKDGSEI 101
R K K G L TLS RY GS I
Sbjct: 209 DLRNHEAKSLPKNKGERLPSLRWGEALTLSRRYKGKGSYI 248
>gnl|CDD|73191 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases;
Methyl transfer reactions play an important role in many
aspects of biology. Cytosine-specific DNA methylases are
found both in prokaryotes and eukaryotes. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the mammalian genome. These
effects include transcriptional repression via
inhibition of transcription factor binding or the
recruitment of methyl-binding proteins and their
associated chromatin remodeling factors, X chromosome
inactivation, imprinting and the suppression of
parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability..
Length = 275
Score = 48.7 bits (116), Expect = 4e-07
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 1 MKACDFGVPQRRERLYIIDFLNPSVEF---KFPTPLGIKPRLGDILEEHIDDKSTIS 54
+ A D+GVPQ RER++II + FP P K L DIL D+ + +
Sbjct: 143 LNASDYGVPQNRERVFIIGIRKDLILNFFSPFPKPSEKKKTLKDILRIRDPDEPSPT 199
>gnl|CDD|33186 COG3379, COG3379, Uncharacterized conserved protein [Function
unknown].
Length = 471
Score = 25.7 bits (56), Expect = 3.1
Identities = 21/97 (21%), Positives = 34/97 (35%), Gaps = 8/97 (8%)
Query: 9 PQRRERLYIIDFLNPSVEFKFPTPLGIKPRLGDI--------LEEHIDDKSTISNKLWEG 60
P+R + + FL P P +K + + +E H +DK LWE
Sbjct: 116 PKRIKGNLVSGFLTPDKSKAKAYPPELKDEIENTTGNEYVFDVEYHDEDKDIFIEDLWEN 175
Query: 61 HQKRKENNKIAGKGFGYGLFFENSATTNTLSARYYKD 97
+ RKE K + F T+ + +K
Sbjct: 176 TESRKEVVKEYLSPKEWDCFGFVMIGTDRVHHALWKY 212
>gnl|CDD|147573 pfam05461, ApoL, Apolipoprotein L. Apo L belongs to the high
density lipoprotein family that plays a central role in
cholesterol transport. The cholesterol content of
membranes is important in cellular processes such as
modulating gene transcription and signal transduction
both in the adult brain and during neurodevelopment.
There are six apo L genes located in close proximity to
each other on chromosome 22q12 in humans. 22q12 is a
confirmed high-susceptibility locus for schizophrenia
and close to the region associated with velocardiofacial
syndrome that includes symptoms of schizophrenia.
Length = 313
Score = 25.4 bits (56), Expect = 3.7
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 37 PRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAG 72
PRL LEEHI +++++ + H+ +N +A
Sbjct: 68 PRLKAELEEHIRKLRALADQVDKVHRGCTISNVVAS 103
>gnl|CDD|37765 KOG2554, KOG2554, KOG2554, Pseudouridylate synthase [Translation,
ribosomal structure and biogenesis].
Length = 425
Score = 25.0 bits (54), Expect = 4.4
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 15 LYIIDFLNPSVEFKFPT-----PLGIKPRLGDILEEHIDDKSTISNKLWEGHQKRKENN 68
LY DF +VE++ T I + L EH+ + S + N E + +N
Sbjct: 315 LYDCDFHRENVEWRHDTESDQIAPKILKITWENLVEHLQNGSAMENIHEEVLGMAEFSN 373
>gnl|CDD|110864 pfam01903, CbiX, CbiX. The function of CbiX is uncertain, however
it is found in cobalamin biosynthesis operons and so may
have a related function. Some CbiX proteins contain a
striking histidine-rich region at their C-terminus,
which suggests that it might be involved in metal
chelation.
Length = 106
Score = 24.5 bits (54), Expect = 6.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 23 PSVEFKFPTPLGIKPRLGDILEE 45
P +E + PLG P L ++L E
Sbjct: 84 PGIEVHYGRPLGPHPLLAELLAE 106
>gnl|CDD|133371 cd04171, SelB, SelB subfamily. SelB is an elongation factor needed
for the co-translational incorporation of
selenocysteine. Selenocysteine is coded by a UGA stop
codon in combination with a specific downstream mRNA
hairpin. In bacteria, the C-terminal part of SelB
recognizes this hairpin, while the N-terminal part binds
GTP and tRNA in analogy with elongation factor Tu
(EF-Tu). It specifically recognizes the selenocysteine
charged tRNAsec, which has a UCA anticodon, in an EF-Tu
like manner. This allows insertion of selenocysteine at
in-frame UGA stop codons. In E. coli SelB binds GTP,
selenocysteyl-tRNAsec, and a stem-loop structure
immediately downstream of the UGA codon (the SECIS
sequence). The absence of active SelB prevents the
participation of selenocysteyl-tRNAsec in translation.
Archaeal and animal mechanisms of selenocysteine
incorporation are more complex. Although the SECIS
elements have different secondary structures and
conserved elements between archaea and eukaryotes, they
do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 164
Score = 24.4 bits (54), Expect = 6.5
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 3 ACDFGV-PQRRERLYIIDFLN 22
A D G+ PQ RE L I++ L
Sbjct: 83 AADEGIMPQTREHLEILELLG 103
>gnl|CDD|146905 pfam04497, Pox_E2, Poxvirus E2 protein. This family of proteins is
restricted to Poxviridae. It contains the proteins E2
and O1 which are uncharacterized.
Length = 726
Score = 24.3 bits (53), Expect = 7.4
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 8 VPQRRERLYIIDFLNPSV----EFK 28
P + + +ID+LN +V EFK
Sbjct: 212 YPSSNDTIRVIDYLNDAVLSSEEFK 236
>gnl|CDD|48387 cd02140, Nitroreductase_4, Nitroreductase-like family 4. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase..
Length = 192
Score = 24.4 bits (53), Expect = 7.7
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 37 PRLGDILEEHIDDKSTISNKLWEGHQKRKENNKIAGKGFGYG--LFFENSATTNTLSARY 94
+L DI+++ + + K+ G GYG LFFE+ A L ++
Sbjct: 56 EKLWDIVKDTL-------RAIVPAEAFAATKEKLDGFKAGYGTVLFFEDQAVVKGLQEKF 108
Query: 95 --YKD 97
Y D
Sbjct: 109 PLYAD 113
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.139 0.419
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,298,968
Number of extensions: 59628
Number of successful extensions: 127
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 10
Length of query: 101
Length of database: 6,263,737
Length adjustment: 68
Effective length of query: 33
Effective length of database: 4,794,325
Effective search space: 158212725
Effective search space used: 158212725
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 (21.7 bits)
S2: 51 (23.5 bits)