RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17760
(105 letters)
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 26.8 bits (59), Expect = 2.1
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 38 MADSGKRNIPIKLGDFSVIDSEFSNIRERFDAEMRKMEDEMTKFRSE--LMNRESNFFKT 95
+AD+ ++P+KL D + E S++ ER + M ME E+ + E + NR +
Sbjct: 165 LADTIAAHMPLKLADKQSV-LEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVKKQMEK 223
Query: 96 STR 98
S R
Sbjct: 224 SQR 226
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 26.8 bits (59), Expect = 2.3
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 68 DAEMRKMEDEMTKF-RSELMNRESNFFKTS 96
+ E+++ E M + S + + + FKTS
Sbjct: 118 EEEIKRTEMFMKQILNSYIFLKNAKIFKTS 147
>gnl|CDD|219273 pfam07028, DUF1319, Protein of unknown function (DUF1319). This
family contains a number of viral proteins of unknown
function approximately 200 residues long. Family
members seem to be restricted to badnaviruses.
Length = 119
Score = 26.2 bits (58), Expect = 2.8
Identities = 8/42 (19%), Positives = 19/42 (45%)
Query: 53 FSVIDSEFSNIRERFDAEMRKMEDEMTKFRSELMNRESNFFK 94
V I+E A++++++DE+ + EL + +
Sbjct: 37 SRVEIKNLLKIQESQRADLKELKDELRTLKRELTALRKEYLE 78
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 26.5 bits (59), Expect = 3.0
Identities = 14/51 (27%), Positives = 17/51 (33%), Gaps = 9/51 (17%)
Query: 37 SMADSGKRNIPIKLGDFSVIDSEFSNIRERFDAEMRKMEDE-----MTKFR 82
M D PI GDF S I +R +R + D FR
Sbjct: 318 DMPDVAAGAKPILFGDF----SRGYLIVDRKGLTIRVLRDPYTEKDQVGFR 364
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III
(ExoIII)-like apurinic/apyrimidinic (AP) endonucleases.
The ExoIII family AP endonucleases 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, which is then
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, which have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a wide range 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
functional AP endonucleases, for example, APE1/Ref-1 and
Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and
NExo in Neisseria meningitides, and exonuclease III
(ExoIII) and endonuclease IV (EndoIV) in Escherichia
coli. Usually, one of the two is the dominant AP
endonuclease, the other has weak AP endonuclease
activity, but exhibits strong 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, and 3'-phosphatase
activities. Class II AP endonucleases have been
classified into two families, designated ExoIII and
EndoIV, based on their homology to the Escherichia coli
enzymes. This family contains the ExoIII family; the
EndoIV family belongs to a different superfamily.
Length = 251
Score = 25.7 bits (57), Expect = 4.3
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 40 DSGKRNIPIKLGDFSVIDSEFSN---IRERFDAEMRKMEDEMTKFRSELMNRESN 91
DS R I + DF +I+ F N ER D ++R + +F +L R
Sbjct: 88 DSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLR-FYEAFLEFLEKLRKRGKP 141
>gnl|CDD|223503 COG0426, FpaA, Uncharacterized flavoproteins [Energy production and
conversion].
Length = 388
Score = 25.7 bits (57), Expect = 6.0
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 64 RERFDAEMRKMEDEMTKFRSELM 86
RFD ++ ++ +M K+ + LM
Sbjct: 174 DYRFDEDIEELLPDMRKYYANLM 196
>gnl|CDD|233812 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3
family of metallopeptidases contains several distinct
clades. Oligoendopeptidase F as characterized in
Lactococcus, the functionally equivalent
oligoendopeptidase B of group B Streptococcus, and
closely related sequences are described by TIGR00181.
The present family is quite similar but forms a distinct
clade, and a number of species have one member of each.
A greater sequence difference separates members of
TIGR02289, probable oligoendopeptidases of the M3 family
that probably should not be designated PepF.
Length = 587
Score = 25.4 bits (56), Expect = 7.4
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 49 KLGDFSVIDSEFSNIRERFDAEMRKMEDE 77
LG+ + SE F E+ ++ DE
Sbjct: 86 LLGELEALSSEIQQALLFFTLELMRLSDE 114
>gnl|CDD|215960 pfam00509, Hemagglutinin, Haemagglutinin. Hemagglutinin from
influenza virus causes membrane fusion of the viral
membrane with the host membrane. Fusion occurs after the
host cell internalises the virus by endocytosis. The
drop of pH causes release of a hydrophobic fusion
peptide and a large conformational change leading to
membrane fusion.
Length = 550
Score = 25.4 bits (56), Expect = 7.5
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 53 FSVIDSEFSNIRERFDAEMRKMEDEMT 79
F I+ EFS + R + +K++D +T
Sbjct: 391 FEAIEKEFSELERRINNLNKKVDDGIT 417
>gnl|CDD|151789 pfam11348, DUF3150, Protein of unknown function (DUF3150). This
bacterial family of proteins with unknown function
appears to be restricted to Proteobacteria.
Length = 257
Score = 25.3 bits (56), Expect = 7.8
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 44 RNIPIKLGDFSVIDSEFSNIRERFDAEMRKMEDE 77
R I KL S +D + + E D + +
Sbjct: 203 RRIRNKLDGLSFLDPRVAPLAEMIDEVLESLPKS 236
>gnl|CDD|226853 COG4445, MiaE, Hydroxylase for synthesis of
2-methylthio-cis-ribozeatin in tRNA [Nucleotide
transport and metabolism / Translation, ribosomal
structure and biogenesis].
Length = 203
Score = 25.2 bits (55), Expect = 7.8
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 37 SMADSGKRNIPIKLGDFSVIDSEFSNIR--ERFDAEMRKMEDEMTKFRSELMNRESNFFK 94
+ + + + P +L D +I + R ERF A +++E+ KF L+ E+ F+
Sbjct: 100 GLLAAVRTHEPQRLID-KLIVGAYIEARSCERFAALAPHLDEELAKFYKGLLRSEARHFQ 158
Query: 95 T 95
Sbjct: 159 D 159
>gnl|CDD|191851 pfam07798, DUF1640, Protein of unknown function (DUF1640). This
family consists of sequences derived from hypothetical
eukaryotic proteins. A region approximately 100
residues in length is featured.
Length = 177
Score = 24.9 bits (55), Expect = 8.0
Identities = 9/31 (29%), Positives = 20/31 (64%), Gaps = 4/31 (12%)
Query: 57 DSEFSNIRERFDAEMRKMEDEMTKFRSELMN 87
SEF+N++ AE K+++++ K ++ L +
Sbjct: 72 KSEFANLQ----AENEKLKNDLEKLKNRLRD 98
>gnl|CDD|224564 COG1650, COG1650, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 266
Score = 24.7 bits (54), Expect = 10.0
Identities = 8/47 (17%), Positives = 18/47 (38%)
Query: 32 RLCLTSMADSGKRNIPIKLGDFSVIDSEFSNIRERFDAEMRKMEDEM 78
++ + S +D NI LG+ ++ + + + ED
Sbjct: 2 KVLVLSASDPASMNIAEYLGEDREFKETVVDVLKSGEFYIVATEDTH 48
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
0.324 0.135 0.385
Gapped
Lambda K H
0.267 0.0539 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,063,646
Number of extensions: 410386
Number of successful extensions: 653
Number of sequences better than 10.0: 1
Number of HSP's gapped: 653
Number of HSP's successfully gapped: 40
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.6 bits)