RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2203
(74 letters)
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 89.5 bits (223), Expect = 1e-25
Identities = 40/57 (70%), Positives = 47/57 (82%), Gaps = 1/57 (1%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPI-ENVDVPGCGKA 71
VLCLLNMVTP+EL+D++EYE+I ED+KEEC KYG V S+ IPRP E VDVPG GK
Sbjct: 3 VLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKV 59
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 78.4 bits (193), Expect = 6e-19
Identities = 27/56 (48%), Positives = 40/56 (71%), Gaps = 1/56 (1%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVD-VPGCGK 70
V+ L N+VT D+L D++EYE+I ED+K E +KYG + ++ IPRP + + PG GK
Sbjct: 411 VVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGK 466
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or
P-CIP2, is a serine/threonine protein kinase
functionally related to RNA metabolism and neurite
outgrowth. It contains an N-terminal kinase domain and
a C-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), with high homology to the corresponding motif
of the mammalian U2 small nuclear ribonucleoprotein
auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2).
UHMK1 targets two key regulators of cell proliferation
and migration, the cyclin-dependent kinase (CDK)
inhibitor p27Kip1 and the microtubule-destabilizing
protein stathmin. It plays a critical role during
vascular wound repair by preventing excessive vascular
smooth muscle cell (VSMC) migration into the vascular
lesion. Moreover, UHMK1 may control cell migration and
neurite outgrowth by interacting with and
phosphorylating the splicing factor SF1, thereby
probably contributing to the control of protein
expression. Furthermore, UHMK1 may be functionally
related to microtubule dynamics and axon development.
It localizes to RNA granules, interacts with three
proteins found in RNA granules (KIF3A, NonO, and
eEF1A), and further enhances the local translation.
UHMK1 is highly expressed in regions of the brain
implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 55.8 bits (134), Expect = 3e-12
Identities = 32/55 (58%), Positives = 39/55 (70%), Gaps = 5/55 (9%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVDVPGCGK 70
VL LLN++ L++E+EYEDI EDIKEEC KYG V SL IP+ EN PG G+
Sbjct: 5 VLRLLNVLDDAHLQNEEEYEDIIEDIKEECQKYGPVVSLLIPK--EN---PGKGQ 54
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 48.3 bits (116), Expect = 3e-09
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEI 56
+ L NM P E +++ ++I ED+ EEC+K+G V +++
Sbjct: 3 CVILKNMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKV 43
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 44.5 bits (106), Expect = 6e-08
Identities = 16/36 (44%), Positives = 24/36 (66%), Gaps = 5/36 (13%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIV 51
+L L NMVTP E+ ++ + ++I+EEC KYG V
Sbjct: 3 ILVLRNMVTPGEIDEDLK-----DEIEEECEKYGKV 33
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal
region, followed by a G-patch motif and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors a RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain)
and an Arg-Xaa-Phe sequence motif. SPF45 regulates
alternative splicing of the apoptosis regulatory gene
FAS (also known as CD95). It induces exon 6 skipping in
FAS pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 39.6 bits (93), Expect = 8e-06
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSL---EIPRP 59
V+ L NMV P E+ ++ E E +KEEC+KYG V + EIP
Sbjct: 4 VVLLRNMVGPGEVDEDLEPE-----VKEECSKYGKVTKVLIFEIPGA 45
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 39.1 bits (91), Expect = 4e-05
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 17 LCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIV 51
L L NM P ++ + +I +D+KEEC+KYG V
Sbjct: 365 LVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGV 399
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 37.6 bits (88), Expect = 5e-05
Identities = 12/42 (28%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 16 VLCLLNMVTPDELKDEDE-YEDICEDIKEECNKYGIVRSLEI 56
V+ L N+ +P+E +++ ++ +D++EEC K+G V+ + +
Sbjct: 3 VVILKNLFSPEEFEEDPTLINELRDDLREECEKFGQVKKVVV 44
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 38.9 bits (90), Expect = 5e-05
Identities = 18/45 (40%), Positives = 28/45 (62%), Gaps = 5/45 (11%)
Query: 7 RLVPPLRFSVLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIV 51
+L+ R +V+ L NMVTP +D E + +I+EEC K+G+V
Sbjct: 507 KLMRTNRSNVIVLRNMVTP-----QDIDEFLEGEIREECGKFGVV 546
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. The research indicates that
PUF60 binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 98
Score = 37.4 bits (87), Expect = 5e-05
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 16 VLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIV 51
V+ L NMV P++L D+ E ++ EEC K+G V
Sbjct: 3 VMVLRNMVGPEDLDDDLE-----GEVTEECGKFGAV 33
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 29.8 bits (68), Expect = 0.074
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 8 LVPPLRFSVLCLLNMVTPDEL 28
L P L V LLN +TPD L
Sbjct: 176 LAPSLDPDVGVLLN-LTPDHL 195
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor
U2AF 35 kDa subunit B (U2AF35B). This subgroup
corresponds to the RRM of U2AF35B, also termed zinc
finger CCCH domain-containing protein 60 (C3H60), which
is one of the small subunits of U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF). It
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs and is a highly conserved heterodimer
composed of large and small subunits. Members in this
family are mainly found in plant. They show high
sequence homology to vertebrates U2AF35 that directly
binds to the 3' splice site of the conserved AG
dinucleotide and performs multiple functions in the
splicing process in a substrate-specific manner.
U2AF35B contains two N-terminal zinc fingers, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal arginine/serine (SR)-rich domain. In
contrast to U2AF35, U2AF35B has a plant-specific
conserved C-terminal region containing SERE motif(s),
which may have an important function specific to higher
plants. .
Length = 103
Score = 28.5 bits (64), Expect = 0.13
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 26 DELKDEDEYEDICEDIKEECNKYGIVRSLEI 56
D + ++ +ED EDI EE +K+G V +L +
Sbjct: 28 DPRELQEHFEDFYEDIFEELSKFGEVEALNV 58
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small
nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa
subunit (U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer
composed of large and small subunits; this family
includes the small subunit of U2AF (U2AF35 or U2AF1)
and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35
directly binds to the 3' splice site of the conserved
AG dinucleotide and performs multiple functions in the
splicing process in a substrate-specific manner. It
promotes U2 snRNP binding to the branch-point sequences
of introns through association with the large subunit
of U2AF (U2AF65 or U2AF2). Although the biological role
of U2AF35B remains unclear, it shows high sequence
homolgy to U2AF35, which contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR) -rich segment interrupted by
glycines. In contrast to U2AF35, U2AF35B has a
plant-specific conserved C-terminal region containing
SERE motif(s), which may have an important function
specific to higher plants. .
Length = 102
Score = 28.4 bits (64), Expect = 0.15
Identities = 6/31 (19%), Positives = 18/31 (58%)
Query: 26 DELKDEDEYEDICEDIKEECNKYGIVRSLEI 56
E + ++ +++ ED+ E +++G + L +
Sbjct: 27 SEEEIQEHFDEFYEDVFLELSRFGEIEDLVV 57
>gnl|CDD|215094 PLN00188, PLN00188, enhanced disease resistance protein (EDR2);
Provisional.
Length = 719
Score = 27.9 bits (62), Expect = 0.44
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 21 NMVTPDELKDEDEYEDICE-DIKEECNKYGIVRSLEIPRPIENVDV 65
N V DE D+DE I E + + E K + P + +D+
Sbjct: 437 NSVMMDEDSDDDEEFQIPESEQEPETTKNETKDTAMEEEPQDKIDL 482
>gnl|CDD|237506 PRK13785, PRK13785, adenylosuccinate synthetase; Provisional.
Length = 454
Score = 27.4 bits (61), Expect = 0.52
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 24 TPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVDVP 66
TPDE DE E++ I+EE +YG V PR + +D+P
Sbjct: 297 TPDEGGRPDE-EELATYIREEGGEYGTVTGR--PRRVGWLDMP 336
>gnl|CDD|183392 PRK12271, rps10p, 30S ribosomal protein S10P; Reviewed.
Length = 102
Score = 26.8 bits (60), Expect = 0.56
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 30 DEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVDVP------GCGKAT 72
+ ++ +++C+ IKE K G+ S IP P + + VP G G AT
Sbjct: 12 NPEDLDEVCDQIKEIAEKTGVDMSGPIPLPTKRLVVPTRKSPDGEGTAT 60
>gnl|CDD|100037 cd06061, PurM-like1, AIR synthase (PurM) related protein, subgroup
1 of unknown function. The family of PurM related
proteins includes Hydrogen expression/formation protein
HypE, AIR synthases, FGAM synthase and Selenophosphate
synthetase (SelD). They all contain two conserved
domains and seem to dimerize. The N-terminal domain
forms the dimer interface and is a putative ATP binding
domain.
Length = 298
Score = 27.2 bits (61), Expect = 0.69
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 9 VPPLRFSVLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGI 50
P V LL P DE+E + I +I E + G+
Sbjct: 76 ARPRWLLVTLLL----PPGT-DEEELKAIMREINEAAKELGV 112
>gnl|CDD|131466 TIGR02413, Bac_small_yrzI, Bacillus tandem small hypothetical
protein. Members of this family are very small
proteins, about 47 residues each, in the genus
Bacillus. Single members are found in Bacillus subtilis
and Bacillus halodurans, but arrays of six in tandem in
Bacillus cereus and Bacillus anthracis. An EIxxE motif
present in most members of this family resembles
cleavage sites by the germination protease GPR in a
number small, acid-soluble spore proteins (SASP). A
role in sporulation is possible.
Length = 46
Score = 25.9 bits (57), Expect = 0.72
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 21 NMVTPDELKDEDEYEDICEDIKEECNKY 48
++ E++ E + E I +++KE + Y
Sbjct: 15 RKLSEAEIEREQQIEKIMDEVKERQSLY 42
>gnl|CDD|235583 PRK05731, PRK05731, thiamine monophosphate kinase; Provisional.
Length = 318
Score = 27.1 bits (61), Expect = 0.75
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 18 CLLNMVTPDELKDEDEYEDICEDIKEECNKYGI 50
LL + P +L DE E + + + E ++YG
Sbjct: 84 FLLALALPKDL-DEAWLEALADGLFELADRYGA 115
>gnl|CDD|206759 cd10023, 14-3-3_theta, 14-3-3 theta/tau (theta in mice, tau in
human), an isoform of 14-3-3 protein. 14-3-3 tau/theta
(tau in humans, theta in mice) isoform (also known as
tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase
activation protein, theta polypeptide) is encoded by the
YWHAQ gene in humans and plays an important role in
controlling apoptosis through interactions with ASK1,
c-jun NH-terminal kinase, and p38 mitogen-activated
protein kinase (MAPK). Its interaction with CDC25c
regulates entry into the cell cycle and subsequent
interaction with Bad prevents apoptosis. 14-3-3 theta
protein expression is induced in patients with
amyotrophic lateral sclerosis. 14-3-3 tau is often
overexpressed in breast cancer, which is associated with
the downregulation of p21, a p53 target gene, and thus
leads to tamoxifen resistance in MCF7 breast cancer
cells and shorter patient survival. Therefore, 14-3-3
tau may be a potential therapeutic target in breast
cancer. Additionally, 14-3-3 theta mediates
nucleocytoplasmic shuttling of the coronavirus
nucleocapsid protein which causes severe acute
respiratory syndrome. 14-3-3 domain is an essential part
of 14-3-3 proteins, a ubiquitous class of regulatory,
phosphoserine/threonine-binding proteins found in all
eukaryotic cells, including yeast, protozoa and
mammalian cells.
Length = 234
Score = 27.0 bits (59), Expect = 0.79
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 20 LNMVTPDELKDEDEYEDICEDIKEECNKYGIVRS 53
L +V K E E IC + E +KY I +
Sbjct: 76 LQLVKDYREKVESELRSICTTVLELLDKYLIANA 109
>gnl|CDD|130118 TIGR01046, S10_Arc_S20_Euk, ribosomal protein
S10(archaeal)/S20(eukaryotic). This model describes
the archaeal ribosomal protein and its equivalents in
eukaryotes [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 99
Score = 25.9 bits (57), Expect = 1.3
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 30 DEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVDVP 66
+ E +C IK K G+ S +P P + + VP
Sbjct: 11 NVRSLEKVCAQIKRIAEKTGVRMSGPVPLPTKRLRVP 47
>gnl|CDD|214701 smart00506, A1pp, Appr-1"-p processing enzyme. Function determined
by Martzen et al. Extended family detected by reciprocal
PSI-BLAST searches (unpublished results, and Pehrson &
Fuji).
Length = 133
Score = 26.1 bits (58), Expect = 1.4
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 5/46 (10%)
Query: 17 LCLLNMVTPDELKDEDEYEDICE----DIKEECNKYGIVRSLEIPR 58
+++ V P E ++ E + E + GI S+ +P
Sbjct: 72 KYVIHAVGPRASGHSKEGFELLENAYRNCLELAIELGI-TSVALPL 116
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 25.4 bits (56), Expect = 1.5
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 38 CEDIKEECNKYGIVRSLEIPRP 59
E+++ +YG+V ++I RP
Sbjct: 16 EEELRRAFERYGVVEDVDIKRP 37
>gnl|CDD|100030 cd02194, ThiL, ThiL (Thiamine-monophosphate kinase) plays a dual
role in de novo biosynthesis and in salvage of exogenous
thiamine. Thiamine salvage occurs in two steps, with
thiamine kinase catalyzing the formation of thiamine
phosphate, and ThiL catalyzing the conversion of this
intermediate to thiamine pyrophosphate. The N-terminal
domain of ThiL binds ATP and is related to the
ATP-binding domains of hydrogen expression/formation
protein HypE, the AIR synthases, FGAM synthase and
selenophosphate synthetase (SelD).
Length = 291
Score = 26.0 bits (58), Expect = 1.6
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 18 CLLNMVTPDELKDEDEYEDICEDIKEECNKYGI 50
LL++ P + DE+ E+ + E ++YG+
Sbjct: 81 FLLSLGLPPDT-DEEWLEEFYRGLAEAADRYGV 112
>gnl|CDD|235821 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
Length = 304
Score = 26.0 bits (58), Expect = 1.6
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 2/48 (4%)
Query: 17 LCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVD 64
L L T EL + +Y + + EE + + + +E V
Sbjct: 192 LTALLGCTNGELLADPDYRALIRALMEEV--AAVAEAEGVHLSVEEVR 237
>gnl|CDD|236580 PRK09593, arb, 6-phospho-beta-glucosidase; Reviewed.
Length = 478
Score = 26.0 bits (57), Expect = 1.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 26 DELKDEDEYEDICEDIKEECNKYGI 50
DEL+ + EDI +EC+KYGI
Sbjct: 104 DELEPNEAGLQFYEDIFKECHKYGI 128
>gnl|CDD|219498 pfam07651, ANTH, ANTH domain. AP180 is an endocytotic accessory
proteins that has been implicated in the formation of
clathrin-coated pits. The domain is involved in
phosphatidylinositol 4,5-bisphosphate binding and is a
universal adaptor for nucleation of clathrin coats.
Length = 278
Score = 26.1 bits (58), Expect = 1.6
Identities = 16/50 (32%), Positives = 18/50 (36%), Gaps = 10/50 (20%)
Query: 19 LLNMVTPDELKDEDEYEDIC-------EDIK---EECNKYGIVRSLEIPR 58
LL D D I E +K E C G RSLEIP+
Sbjct: 211 LLEKFFEMSKPDADAALGIYKRFVSQFERLKEFYEVCKNLGYFRSLEIPK 260
>gnl|CDD|205568 pfam13390, DUF4108, Protein of unknown function (DUF4108). This
family of putative proteins are found in Trichomonas
vaginalis in large numbers. The function of this protein
is unknown.
Length = 136
Score = 25.6 bits (56), Expect = 1.9
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 5 WDRLVPPLRFSVLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGI----VRSLEIPRPI 60
+DR L+ L V P E K D+YE + E K G + + P+
Sbjct: 71 FDRRFSNLKEGKAYKL--VIPYEPKKADDYEYYESKVVEVQGKLGKKILESKPVFAPKEE 128
Query: 61 ENVDV 65
EN+D+
Sbjct: 129 ENIDI 133
>gnl|CDD|179366 PRK02102, PRK02102, ornithine carbamoyltransferase; Validated.
Length = 331
Score = 25.6 bits (57), Expect = 2.2
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 22 MVTPDELKDEDEYEDICEDIKEE 44
+ P EL E+E + +I +E
Sbjct: 185 ICAPKELWPEEELVALAREIAKE 207
>gnl|CDD|176543 cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase
domain of Staphylococcus aureus and similar proteins.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized glycerophosphodiester phosphodiesterase
(GP-GDE, EC 3.1.4.46) from Staphylococcus aureus,
Bacillus subtilis and similar proteins. Members in this
family show very high sequence similarity to Escherichia
coli periplasmic phosphodiesterase GlpQ, which catalyzes
the Ca2+-dependent degradation of periplasmic
glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 256
Score = 25.7 bits (57), Expect = 2.2
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 27 ELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPI 60
E K D Y + E + +KYG++ +
Sbjct: 117 ETKSPDLYPGMEEKLLATLDKYGLLTDNLKNGQV 150
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes
including mRNA and rRNA processing, RNA export, and RNA
stability. This domain is 90 amino acids in length and
consists of a four-stranded beta-sheet packed against
two alpha-helices. RRM usually interacts with ssRNA,
but is also known to interact with ssDNA as well as
proteins. RRM binds a variable number of nucleotides,
ranging from two to eight. The active site includes
three aromatic side-chains located within the conserved
RNP1 and RNP2 motifs of the domain. The RRM domain is
found in a variety heterogeneous nuclear
ribonucleoproteins (hnRNPs), proteins implicated in
regulation of alternative splicing, and protein
components of small nuclear ribonucleoproteins
(snRNPs).
Length = 72
Score = 25.0 bits (55), Expect = 2.2
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 39 EDIKEECNKYGIVRSLEIPR 58
ED++E +K+G + S+ I R
Sbjct: 13 EDLRELFSKFGEIESVRIVR 32
>gnl|CDD|153245 cd07983, LPLAT_DUF374-like, Lysophospholipid Acyltransferases
(LPLATs) of Glycerophospholipid Biosynthesis: DUF374.
Lysophospholipid acyltransferase (LPLAT) superfamily
member: acyltransferases of de novo and remodeling
pathways of glycerophospholipid biosynthesis which
catalyze the incorporation of an acyl group from either
acylCoAs or acyl-acyl carrier proteins (acylACPs) into
acceptors such as glycerol 3-phosphate, dihydroxyacetone
phosphate or lyso-phosphatidic acid. Included in this
subgroup are the uncharacterized DUF374
phospholipid/glycerol acyltransferases and similar
proteins.
Length = 189
Score = 25.6 bits (57), Expect = 2.4
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 5 WDRLVPPLRFS--VLCLLNMVTPDELKDEDEYEDICE 39
WDR + P FS V+ + DE+E E+
Sbjct: 145 WDRFIIPKPFSRVVIVFGEPIHVPPDADEEELEEYRL 181
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 24.9 bits (55), Expect = 2.5
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 39 EDIKEECNKYGIVRSLEIPR 58
E+++E +K+G V S+ + R
Sbjct: 14 EELRELFSKFGKVESVRLVR 33
>gnl|CDD|233387 TIGR01379, thiL, thiamine-monophosphate kinase. This model
describes thiamine-monophosphate kinase, an enzyme that
converts thiamine monophosphate into thiamine
pyrophosphate (TPP, coenzyme B1), an enzyme cofactor.
Thiamine monophosphate may be derived from de novo
synthesis or from unphosphorylated thiamine, known as
vitamin B1. Proteins scoring between the trusted and
noise cutoff for this model include short forms from the
Thermoplasmas (which lack the N-terminal region) and a
highly derived form from Campylobacter jejuni.
Eukaryotes lack this enzyme, and add pyrophosphate from
ATP to unphosphorylated thiamine in a single step
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 317
Score = 25.4 bits (56), Expect = 2.6
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 18 CLLNMVTPDELKDEDEYEDICEDIKEECNKYGI 50
LL++ P +L DE E + + E +YG+
Sbjct: 82 FLLSLGLPSDL-DEAWLEAFYDGLFEAAKQYGV 113
>gnl|CDD|215557 PLN03069, PLN03069, magnesiumprotoporphyrin-IX chelatase subunit
H; Provisional.
Length = 1220
Score = 25.5 bits (56), Expect = 2.6
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 26 DELKDEDEYEDICEDIKE 43
+EL+D D YE +D+++
Sbjct: 62 EELRDADNYETFKKDVED 79
>gnl|CDD|216703 pfam01791, DeoC, DeoC/LacD family aldolase. This family includes
diverse aldolase enzymes. This family includes the
enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which
is involved in nucleotide metabolism. The family also
includes a group of related bacterial proteins of
unknown function. The family also includes tagatose
1,6-diphosphate aldolase (EC:4.1.2.40) is part of the
tagatose-6-phosphate pathway of galactose-6-phosphate
degradation.
Length = 231
Score = 25.4 bits (56), Expect = 2.6
Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 26 DELKDEDE---YEDICEDIKEECNKYGIVRSLEI-PRPIENVD 64
EDE +I +KE C+ G+ LE R E D
Sbjct: 98 GADGSEDEEQVLAEI-AAVKEACHGEGLKVILEAYLRGEEIKD 139
>gnl|CDD|216008 pfam00586, AIRS, AIR synthase related protein, N-terminal domain.
This family includes Hydrogen expression/formation
protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase
EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The
N-terminal domain of AIR synthase forms the dimer
interface of the protein, and is suggested as a
putative ATP binding domain.
Length = 96
Score = 24.8 bits (55), Expect = 2.8
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 17 LCLLNMVTPDELKDEDEYEDICEDIKEECNKYGI 50
L LL+ + E D + E+I I E N++G+
Sbjct: 56 LALLDGLALGEGLDPEWLEEIVRGIAEAANEFGV 89
>gnl|CDD|237324 PRK13266, PRK13266, Thf1-like protein; Reviewed.
Length = 225
Score = 25.3 bits (56), Expect = 2.8
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 19 LLNMVTPDELKDEDEYEDICEDIKE 43
LL PD +KDE++ + +DI E
Sbjct: 151 LLEEAQPDLVKDEEKLNEALKDISE 175
>gnl|CDD|238621 cd01296, Imidazolone-5PH,
Imidazolonepropionase/imidazolone-5-propionate hydrolase
(Imidazolone-5PH) catalyzes the third step in the
histidine degradation pathway, the hydrolysis of
(S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to
N-formimidoyl-L-glutamate. In bacteria, the enzyme is
part of histidine utilization (hut) operon.
Length = 371
Score = 25.3 bits (56), Expect = 3.2
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 10/56 (17%)
Query: 11 PLRFSVLCLLNMVTPDELKDEDEY-EDICEDIKEECNKYGIVRSLEIPRPIENVDV 65
P+ L P E K +EY + + E++ + + + DV
Sbjct: 137 PVDLVSTFLGAHAVPPEYKGREEYIDLVIEEVLPAVAEENLA---------DFCDV 183
>gnl|CDD|225054 COG2143, COG2143, Thioredoxin-related protein [Posttranslational
modification, protein turnover, chaperones].
Length = 182
Score = 25.2 bits (55), Expect = 3.5
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 9 VPPLRFSVLCLLNMVTPDELKDEDEYEDICEDIKEECNK 47
+PP +F L +L V + KD ED + +K
Sbjct: 136 MPPEQF--LAVLKYVADGKYKDTKTDEDFTKKLKAYIKY 172
>gnl|CDD|233094 TIGR00693, thiE, thiamine-phosphate pyrophosphorylase. This
model represents the thiamine-phosphate
pyrophosphorylase, ThiE, of a number of bacteria, and
N-terminal domains of bifunctional thiamine proteins of
Saccharomyces cerevisiae and Schizosaccharomyces pombe,
in which the C-terminal domain corresponds to the
bacterial hydroxyethylthiazole kinase (EC 2.7.1.50),
ThiM. This model includes ThiE from Bacillus subtilis
but excludes its paralog, the regulatory protein TenI ,
and neighbors of TenI [Biosynthesis of cofactors,
prosthetic groups, and carriers, Thiamine].
Length = 196
Score = 24.9 bits (55), Expect = 3.6
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 26 DELKDEDEYEDICEDIKEECNKYGI 50
D+ + E + E ++E C +YG+
Sbjct: 34 DKGSNTRERLALAEKLQELCRRYGV 58
>gnl|CDD|236453 PRK09287, PRK09287, 6-phosphogluconate dehydrogenase; Validated.
Length = 459
Score = 25.1 bits (56), Expect = 3.7
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 28 LKDEDEYEDI--CEDIKEECNKYGIVRSLEIPRPI 60
L +E + + I ++E V SLE PR I
Sbjct: 30 LAEEGKGKKIVPAYTLEE------FVASLEKPRKI 58
>gnl|CDD|227904 COG5617, COG5617, Predicted integral membrane protein [Function
unknown].
Length = 801
Score = 25.1 bits (55), Expect = 3.7
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 10/39 (25%)
Query: 1 MYPPWDRL----VPPLRFS------VLCLLNMVTPDELK 29
YPPW P LR+ + LN + D +
Sbjct: 52 WYPPWCEYWYNGYPFLRYYPPLSYLIGAALNFLLGDVVT 90
>gnl|CDD|204462 pfam10361, DUF2434, Protein of unknown function (DUF2434). This is
a family of proteins conserved in fungi. The function is
not known.
Length = 296
Score = 25.0 bits (55), Expect = 3.8
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 5 WDRLVPPLRFSVLCLLNMV 23
L P+ F V LLN
Sbjct: 170 RQELYLPIVFYVFALLNFF 188
>gnl|CDD|236364 PRK09034, PRK09034, aspartate kinase; Reviewed.
Length = 454
Score = 25.1 bits (56), Expect = 4.0
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 26 DELKDEDEYEDICEDIKEECN 46
+L + E E I +IK+E N
Sbjct: 356 RQLTPKKEDE-ILAEIKQELN 375
>gnl|CDD|223429 COG0352, ThiE, Thiamine monophosphate synthase [Coenzyme
metabolism].
Length = 211
Score = 24.9 bits (55), Expect = 4.3
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 29 KDEDEYEDICEDIKEECNKYGI 50
++EY + E ++ C KYG+
Sbjct: 45 LSDEEYLALAEKLRALCQKYGV 66
>gnl|CDD|179391 PRK02240, PRK02240, GTP cyclohydrolase III; Provisional.
Length = 254
Score = 24.9 bits (55), Expect = 4.6
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 30 DEDEYEDICEDIKEECN---KYGIVR 52
E ++ D E ++EE K GI R
Sbjct: 197 SEGDFLDAIEHVREEVGVELKVGIGR 222
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 24.6 bits (54), Expect = 5.2
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 15 SVLCLLNMVTPDELKDEDEYEDICEDIKEECNKYGIVRSLEIPRPIENVDVPGCGK 70
+++ L ++ EL D YE +CE ++ ++ + S I + + G+
Sbjct: 287 AIVELTVEISTGEL--YDVYESLCERLRTSQRRFSDIISELEGLGIVSASLISRGE 340
>gnl|CDD|222883 PHA02572, nrdA, ribonucleoside-diphosphate reductase subunit alpha;
Provisional.
Length = 753
Score = 24.7 bits (54), Expect = 5.3
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 17 LCLLNMVTPDELKDEDEYEDICE 39
LC L+ + +D+DE E++ E
Sbjct: 456 LCTLSAIVLGNFEDQDEIEELAE 478
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 24.7 bits (54), Expect = 6.0
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 19 LLNMVTPDELKDEDEYEDICEDIKEECNKYGIVR 52
L+N+ PD+ K E Y+ +D++ C + GI
Sbjct: 202 LINLANPDKEKREKSYDAFLDDLQ-RCEQLGIKL 234
>gnl|CDD|217739 pfam03802, CitX, Apo-citrate lyase phosphoribosyl-dephospho-CoA
transferase.
Length = 171
Score = 24.5 bits (54), Expect = 6.0
Identities = 4/28 (14%), Positives = 9/28 (32%)
Query: 20 LNMVTPDELKDEDEYEDICEDIKEECNK 47
L + P +KD + + +
Sbjct: 33 LTLNIPGPVKDNPLLRRVFDAGLQALEA 60
>gnl|CDD|235394 PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1290
Score = 24.4 bits (54), Expect = 7.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 57 PRPIENVDVPGCGKATLV 74
P+P+ +VDV G G+A L
Sbjct: 151 PKPLTSVDVLGGGRAALE 168
>gnl|CDD|180509 PRK06285, PRK06285, chorismate mutase; Provisional.
Length = 96
Score = 23.8 bits (52), Expect = 7.4
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 27 ELKDEDEYEDICEDIKEECNKYGI 50
+ D + + I E I++ C ++ I
Sbjct: 47 PIFDPEREDYIHEKIRKLCEEHNI 70
>gnl|CDD|238993 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer.
Length = 179
Score = 24.1 bits (53), Expect = 8.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 19 LLNMVTPDELKDEDEYEDICEDIK 42
++N V PD ++ D EDI E +
Sbjct: 120 IVNRVRPDMVEGGDMVEDIEEILG 143
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 23.8 bits (52), Expect = 10.0
Identities = 8/26 (30%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 18 CLLNMVTPDELKDEDEYEDICEDIKE 43
L +V+ ++L++ Y + EDI+E
Sbjct: 492 SLATLVSEEDLREGKLYPPL-EDIRE 516
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
0.320 0.144 0.459
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,958,569
Number of extensions: 310290
Number of successful extensions: 692
Number of sequences better than 10.0: 1
Number of HSP's gapped: 687
Number of HSP's successfully gapped: 61
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)