RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5982
(102 letters)
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 78.9 bits (195), Expect = 8e-19
Identities = 34/47 (72%), Positives = 42/47 (89%)
Query: 4 KKKTALGRLKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVAW 50
KKK + RL+E++ KLEVQ TDKEENKT+ALGTSK+NY+DPRI+VAW
Sbjct: 340 KKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAW 386
>gnl|CDD|206538 pfam14370, Topo_C_assoc, C-terminal topoisomerase domain. This
domain is found at the C-terminal of topoisomerase and
other similar enzymes.
Length = 71
Score = 72.3 bits (178), Expect = 2e-18
Identities = 28/39 (71%), Positives = 36/39 (92%)
Query: 12 LKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVAW 50
L+E++ KLE+Q DKEENKT+ALGTSK+NY+DPRI+VAW
Sbjct: 1 LEERIKKLELQLKDKEENKTVALGTSKINYIDPRITVAW 39
>gnl|CDD|238355 cd00659, Topo_IB_C, DNA topoisomerase IB, C-terminal catalytic
domain. Topoisomerase I promotes the relaxation of both
positive and negative DNA superhelical tension by
introducing a transient single-stranded break in duplex
DNA. This function is vital for the processes of
replication, transcription, and recombination. Unlike
Topo IA enzymes, Topo IB enzymes do not require a
single-stranded region of DNA or metal ions for their
function. The type IB family of DNA topoisomerases
includes eukaryotic nuclear topoisomerase I,
topoisomerases of poxviruses and bacterial versions of
Topo IB. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their C-terminal catalytic domain and the overall
reaction mechanism with tyrosine recombinases. The
C-terminal catalytic domain in topoisomerases is linked
to a divergent N-terminal domain that shows no sequence
or structure similarity to the N-terminal domains of
tyrosine recombinases.
Length = 218
Score = 32.2 bits (74), Expect = 0.022
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 35 GTSKLNYLDPRISVAW 50
SK+NY+DPRI+VAW
Sbjct: 199 AISKINYIDPRITVAW 214
>gnl|CDD|241262 cd01228, PH_BCR-related, Breakpoint Cluster Region-related
pleckstrin homology (PH) domain. The BCR gene is one of
the two genes in the BCR-ABL complex, which is
associated with the Philadelphia chromosome, a product
of a reciprocal translocation between chromosomes 22 and
9. BCR is a GTPase-activating protein (GAP) for RAC1
(primarily) and CDC42. The Dbl region of BCR has the
most RhoGEF activity for Cdc42, and less activity
towards Rac and Rho. Since BCR possesses both GAP and
GEF activities, it may function to temporally regulate
the activity of these GTPases. It also displays
serine/threonine kinase activity. The BCR protein
contains multiple domains including an N-terminal kinase
domain, a RhoGEF domain, a PH domain, a C1 domain, a C2
domain, and a C-terminal RhoGAP domain. ABR, a related
smaller protein, is structurally similar to BCR, but
lacks the N-terminal kinase domain and has GAP activity
for both Rac and Cdc42. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 179
Score = 27.3 bits (61), Expect = 1.3
Identities = 10/69 (14%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 2 TDKKKTALGRLKEQLLKLEVQETDKEE------NKTIALGTSKLNYLDPRISVAWYNLGF 55
+ ++ + + L + +++ + + ++ I KL + + +A +L
Sbjct: 87 SSEELVQMKKAISALKQKIKRDSAERKKAASSGSRAIEKLRKKLAEQEAALLLASPSLPL 146
Query: 56 DFYNWSGKT 64
Y+ +GKT
Sbjct: 147 RLYHRNGKT 155
>gnl|CDD|176680 cd07257, THT_oxygenase_C, The C-terminal domain of
2,4,5-Trihydroxytoluene (THT) oxygenase, which is an
extradiol dioxygenease in the 2,4-dinitrotoluene (DNT)
degradation pathway. This subfamily contains the
C-terminal, catalytic, domain of THT oxygenase. THT
oxygenase is an extradiol dioxygenase in the
2,4-dinitrotoluene (DNT) degradation pathway. It
catalyzes the conversion of 2,4,5-trihydroxytoluene to
an unstable ring fission product,
2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The
native protein was determined to be a dimer by gel
filtration. The enzyme belongs to the type I family of
extradiol dioxygenases which contains two structurally
homologous barrel-shaped domains at the N- and
C-terminus of each monomer. The active-site metal is
located in the C-terminal barrel. Fe(II) is required
for its catalytic activity.
Length = 153
Score = 26.1 bits (58), Expect = 2.9
Identities = 9/40 (22%), Positives = 11/40 (27%), Gaps = 6/40 (15%)
Query: 34 LGTSKLNYLDPRISVAWY--NLGF---DFYNWSGKTKKVI 68
LG L D S WY G D + +
Sbjct: 2 LGHVVLEVPDFAASFDWYTETFGLKPSDVI-YLPGPGNPV 40
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 25.6 bits (57), Expect = 4.1
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 5 KKTALGRLKEQLLKLEVQETDKEENKT 31
++ AL RLK +L + E+Q+ ++ T
Sbjct: 60 REKALERLKAKLYEAELQKKREKTKPT 86
>gnl|CDD|185471 PTZ00136, PTZ00136, eukaryotic translation initiation factor 6-like
protein; Provisional.
Length = 247
Score = 25.1 bits (55), Expect = 7.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 74 NSLPSQAIKRRIDWDLSGLPNTRIAN 99
NSLP +R++ LS L N N
Sbjct: 86 NSLPDSVKVQRVEERLSALGNCIACN 111
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
0.313 0.131 0.380
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,066,595
Number of extensions: 409919
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 20
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)