RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2291
(96 letters)
>gnl|CDD|218993 pfam06331, Tbf5, Transcription factor TFIIH complex subunit Tfb5.
This family is a component of the general
transcription and DNA repair factor IIH. TFB5 has been
shown to be required for efficient recruitment of TFIIH
to a promoter.
Length = 68
Score = 66.8 bits (164), Expect = 2e-16
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPIND 94
D +KQ +LH+DE G FII+DLD+THL + V+E L ++ LL++ + +
Sbjct: 13 DPSIKQIILHIDEQEHHG--FIIEDLDDTHLLVKESVVEFLKEELERLLEENIYNPTE 68
>gnl|CDD|187795 cd09664, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily
protein Cas6e. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas6e is an endoribonuclease that generates crRNA; This
family is specific for CRISPR/Cas system I-E subtype;
Homologous to Cas6 (RAMP superfamily protein);
Possesses double RRM/ferredoxin fold; also known as
Cse3 family.
Length = 210
Score = 26.8 bits (59), Expect = 1.5
Identities = 10/65 (15%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 14 KQFLLHLDETNTLG-RRFIIHCFSDKP--MKQFLLHLDETNTLGRRFIIQDLDETHLFIS 70
L + +++ F D +QFL + + G + ++
Sbjct: 11 ADLAAALRSADPYSLHQWLWSLFPDVEAEKRQFLFRDEGGDAKGGKVLVLSARPPLQSAY 70
Query: 71 SDVIE 75
+ VIE
Sbjct: 71 AFVIE 75
>gnl|CDD|217685 pfam03712, Cu2_monoox_C, Copper type II ascorbate-dependent
monooxygenase, C-terminal domain. The N and C-terminal
domains of members of this family adopt the same PNGase
F-like fold.
Length = 157
Score = 26.5 bits (59), Expect = 1.8
Identities = 12/50 (24%), Positives = 16/50 (32%), Gaps = 5/50 (10%)
Query: 1 MEIYCNYVDDKPMKQF--LLHLDETNTLGRRFIIHCFSDKPMKQFLLHLD 48
+E C K M F H T+ LGR + D + D
Sbjct: 25 VEGSCEIECTKTMFPFAYRTH---THLLGRVVSGYLVRDGEEWTLIGRDD 71
>gnl|CDD|215752 pfam00151, Lipase, Lipase.
Length = 329
Score = 25.8 bits (57), Expect = 3.3
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 24 NTLGRRFIIHCFSDKPMKQ 42
+ R IIH F+DK ++
Sbjct: 69 TSKKTRAIIHGFTDKGQEE 87
>gnl|CDD|192931 pfam12068, DUF3548, Domain of unknown function (DUF3548). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 184 to 216 amino acids in length. This domain is
found associated with pfam00566. This domain is found at
the N-terminus of GYP7 proteins.
Length = 210
Score = 25.5 bits (56), Expect = 4.6
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 18 LHLDETNTLGRRFIIHCFSDKPMKQ----FLLHLDETNTLGRRFI 58
+ L E+ R F++ S K + Q LL D + L RF
Sbjct: 164 IILAESPQDSRLFLVVPQSSKALSQSFSNLLLFDDTSYDLVSRFK 208
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type), N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 352
Score = 25.3 bits (56), Expect = 5.0
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLM 78
K L + + +IQ L+E + +++ ++LL
Sbjct: 159 ESDLNKP--LRIFDDTNNKGGVVIQGLEEITVNNANEGLKLLE 199
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 25.5 bits (56), Expect = 5.8
Identities = 16/59 (27%), Positives = 31/59 (52%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPIND 94
+D PM Q H+ +G +I+ L++ + +++EL+ V +LL + FP +D
Sbjct: 109 TDGPMPQTREHILLARQVGVPYIVVFLNKCDMVDDEELLELVEMEVRELLSEYDFPGDD 167
>gnl|CDD|198298 cd03189, GST_C_GTT1_like, C-terminal, alpha helical domain of
GTT1-like Glutathione S-transferases. Glutathione
S-transferase (GST) C-terminal domain family,
Saccharomyces cerevisiae GTT1-like subfamily; composed
of predominantly uncharacterized proteins with
similarity to the S. cerevisiae GST protein, GTT1, and
the Schizosaccharomyces pombe GST-III. GSTs are
cytosolic dimeric proteins involved in cellular
detoxification by catalyzing the conjugation of
glutathione (GSH) with a wide range of endogenous and
xenobiotic alkylating agents, including carcinogens,
therapeutic drugs, environmental toxins, and products
of oxidative stress. GSTs also show GSH peroxidase
activity and are involved in the synthesis of
prostaglandins and leukotrienes. The GST fold contains
an N-terminal thioredoxin-fold domain and a C-terminal
alpha helical domain, with an active site located in a
cleft between the two domains. GSH binds to the
N-terminal domain while the hydrophobic substrate
occupies a pocket in the C-terminal domain. GTT1, a
homodimer, exhibits GST activity with standard
substrates and associates with the endoplasmic
reticulum. Its expression is induced after diauxic
shift and remains high throughout the stationary phase.
S. pombe GST-III is implicated in the detoxification of
various metals.
Length = 123
Score = 25.0 bits (55), Expect = 5.9
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 13 MKQFLLHLDETNTLGRRFIIHCFSDKPMKQFL-----LHLDETNT 52
+K + E R I +DKP++ F+ HLD
Sbjct: 28 LKLVFGKIGEAPPPFFRPISRKIADKPLQAFINPELKRHLDFLED 72
>gnl|CDD|190783 pfam03888, MucB_RseB, MucB/RseB family. Members of this family are
regulators of the anti-sigma E protein RseD.
Length = 285
Score = 25.1 bits (55), Expect = 6.5
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 21/57 (36%)
Query: 42 QFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ---ISFPINDR 95
+ L LDE E+ L + SD L+ R +LL+Q +N R
Sbjct: 124 SYELWLDE--------------ESGLPLRSD----LLDRDGELLEQFRVTQLNVNQR 162
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 24.9 bits (55), Expect = 8.8
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 67 LFISSDVIELLMTRVDDLLD 86
++ D E+L+ RV D+LD
Sbjct: 206 VWYCEDCGEVLVRRVPDVLD 225
>gnl|CDD|189014 cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 581
Score = 24.8 bits (55), Expect = 9.6
Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 8/93 (8%)
Query: 9 DDKPMKQFLLHLDETNTLGRR--FIIHCFSDKPMK--QFLLHLDETNTLGRRFII--QDL 62
+ ++ + L E L R + C + L + N L L
Sbjct: 43 AVETLEALITLLQELLELLRTLGAFVSCLLSADTTDEEAQALLSQLNQLSASLEQLLTLL 102
Query: 63 DETHLFISSDVIELLMTRVDDLLDQISFPINDR 95
D+ +S + ++ L+ D L + +F + +R
Sbjct: 103 DKKLAALSEEDLDALLA--DPELKEHAFFLEER 133
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
0.328 0.146 0.435
Gapped
Lambda K H
0.267 0.0654 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,038,095
Number of extensions: 437876
Number of successful extensions: 495
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 29
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)