RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13847
(91 letters)
>gnl|CDD|199815 cd10491, MH1_SMAD_2_3, N-terminal Mad Homology 1 (MH1) domain in
SMAD2 and SMAD3. The MH1 is a small DNA-binding domain
present in SMAD (small mothers against decapentaplegic)
family of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 is found in
SMAD2 as well as SMAD3. SMAD2 mediates the signal of
the transforming growth factor (TGF)-beta, and thereby
regulates multiple cellular processes, such as cell
proliferation, apoptosis, and differentiation. It plays
a role in the transmission of extracellular signals
from ligands of the TGF-beta superfamily growth factors
into the cell nucleus. SMAD3 modulates signals of
activin and TGF-beta. It binds SMAD4, enabling its
transmigration into the nucleus where it forms
complexes with other proteins and acts as a
transcription factor. Increased SMAD3 activity has been
implicated in the pathogenesis of scleroderma.
Length = 124
Score = 109 bits (275), Expect = 8e-33
Identities = 48/61 (78%), Positives = 55/61 (90%), Gaps = 2/61 (3%)
Query: 8 TPPIVKKLLGWKKG--DGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIP 65
TPP+VK+LLGWKKG E+K+SEKAVKSLVKKLKK+ GLDELEKAITTQ+ NTKC+TIP
Sbjct: 1 TPPVVKRLLGWKKGENGQEEKWSEKAVKSLVKKLKKTGGLDELEKAITTQNSNTKCITIP 60
Query: 66 R 66
R
Sbjct: 61 R 61
>gnl|CDD|199812 cd10488, MH1_R-SMAD, N-terminal Mad Homology 1 (MH1) domain of
receptor regulated SMADs. The MH1 is a small
DNA-binding domain present in SMAD (small mothers
against decapentaplegic) family of proteins, which are
signal transducers and transcriptional modulators that
mediate multiple signaling pathways. It binds to the
major groove in an unusual manner via a beta hairpin
structure. It negatively regulates the functions of
the MH2 domain, the C-terminal domain of SMAD. This MH1
domain is found in all receptor regulated SMADs
(R-SMADs) including SMAD1, SMAD2, SMAD3, SMAD5 and
SMAD9. SMAD1 plays an essential role in bone
development and postnatal bone formation through
activation by bone morphogenetic protein (BMP) type 1
receptor kinase. SMAD2 regulates multiple cellular
processes, such as cell proliferation, apoptosis and
differentiation, while SMAD3 modulates signals of
activin and TGF-beta. SMAD4, a common mediator SMAD
(co-SMAD) binds R-SMADs, forming an oligomeric complex
that binds to DNA and serves as a transcription factor.
SMAD5 is involved in bone morphogenetic proteins (BMP)
signal modulation, possibly playing a role in the
pathway involving inhibition of hematopoietic
progenitor cells by TGF-beta. SMAD9 (also known as
SMAD8) can mediate the differentiation of mesenchymal
stem cells (MSCs) into tendon-like cells by inhibiting
the osteogenic pathway.
Length = 123
Score = 84.5 bits (209), Expect = 7e-23
Identities = 43/60 (71%), Positives = 51/60 (85%), Gaps = 3/60 (5%)
Query: 10 PIVKKLLGWKKG---DGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIPR 66
PIVK+LLGWKKG E+K++EKAVKSLVKKLKK L+ELEKAI+TQ+ NT+CVTIPR
Sbjct: 1 PIVKRLLGWKKGEQNGEEEKWAEKAVKSLVKKLKKKGQLEELEKAISTQNVNTRCVTIPR 60
>gnl|CDD|199814 cd10490, MH1_SMAD_1_5_9, N-terminal Mad Homology 1 (MH1) domain
in SMAD1, SMAD5 and SMAD9 (also known as SMAD8). The
MH1 is a small DNA-binding domain present in SMAD
(small mothers against decapentaplegic) family of
proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 domain is found
in SMAD1, SMAD5 and SMAD9, all closely related receptor
regulated SMADs (R-SMADs). SMAD1 plays an essential
role in bone development and postnatal bone formation
through activation by bone morphogenetic protein (BMP)
type 1 receptor kinase. SMAD5 is involved in bone
morphogenetic proteins (BMP) signal modulation and may
also play a role in the pathway involving inhibition of
hematopoietic progenitor cells by TGF-beta. SMAD9
mediates the differentiation of mesenchymal stem cells
(MSCs) into tendon-like cells by inhibiting the
osteogenic pathway.
Length = 124
Score = 84.1 bits (208), Expect = 1e-22
Identities = 40/61 (65%), Positives = 49/61 (80%), Gaps = 1/61 (1%)
Query: 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNG-LDELEKAITTQDPNTKCVTIP 65
FT P VK+LLGWK+GD E+K++EKAV SLVKKLKK G L+ELEKA++ +KCVTIP
Sbjct: 1 FTSPAVKRLLGWKQGDEEEKWAEKAVDSLVKKLKKKKGALEELEKALSCPGQPSKCVTIP 60
Query: 66 R 66
R
Sbjct: 61 R 61
>gnl|CDD|199811 cd00049, MH1, N-terminal Mad Homology 1 (MH1) domain. The MH1 is
a small DNA-binding domain present in SMAD (small
mothers against decapentaplegic) family of proteins,
which are signal transducers and transcriptional
modulators that mediate multiple signaling pathways.
MH1 binds to the DNA major groove in an unusual manner
via a beta hairpin structure. It negatively regulates
the functions of the MH2 domain, the C-terminal domain
of SMAD. Receptor-regulated SMAD proteins (R-SMADs,
including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are
activated by phosphorylation by transforming growth
factor (TGF)-beta type I receptors. The active R-SMAD
associates with a common mediator SMAD (Co-SMAD or
SMAD4) and other cofactors, which together translocate
to the nucleus to regulate gene expression. The
inhibitory or antagonistic SMADs (I-SMADs, including
SMAD6 and SMAD7) negatively regulate TGF-beta signaling
by competing with R-SMADs for type I receptor or
Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a
nuclear localization signal as well as DNA-binding
activity. The activated R-SMAD/SMAD4 complex then binds
with very low affinity to a DNA sequence CAGAC called
SMAD-binding element (SBE) via the MH1 domain.
Length = 121
Score = 76.5 bits (188), Expect = 9e-20
Identities = 42/68 (61%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 10 PIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDP-NTKCVTIPRLQ 68
PIVK+LLGWK+G E+K+++KAVKSLVKKLK+ LD LEKAITTQ +KCVTIPR
Sbjct: 1 PIVKRLLGWKQGGEEEKWAKKAVKSLVKKLKEKKQLDSLEKAITTQGGVPSKCVTIPRSL 60
Query: 69 FEDLQQSG 76
LQ +
Sbjct: 61 DGRLQVAH 68
>gnl|CDD|217397 pfam03165, MH1, MH1 domain. The MH1 (MAD homology 1) domain is
found at the amino terminus of MAD related proteins
such as Smads. This domain is separated from the MH2
domain by a non-conserved linker region. The crystal
structure of the MH1 domain shows that a highly
conserved 11 residue beta hairpin is used to bind the
DNA consensus sequence GNCN in the major groove, shown
to be vital for the transcriptional activation of
target genes. Not all examples of MH1 can bind to DNA
however. Smad2 cannot bind DNA and has a large
insertion within the hairpin that presumably abolishes
DNA binding. A basic helix (H2) in MH1 with the nuclear
localisation signal KKLKK has been shown to be
essential for Smad3 nuclear import. Smads also use the
MH1 domain to interact with transcription factors such
as Jun, TFE3, Sp1, and Runx.
Length = 103
Score = 52.4 bits (126), Expect = 2e-10
Identities = 27/50 (54%), Positives = 35/50 (70%), Gaps = 2/50 (4%)
Query: 29 EKAVKSLVKKLKKSNG-LDELEKAITTQ-DPNTKCVTIPRLQFEDLQQSG 76
+KAV+SL+KKLKK L+ELE A+ ++ P TKCVTIPR LQ +G
Sbjct: 2 KKAVESLLKKLKKKKQQLEELELAVESRGGPPTKCVTIPRSLDGRLQVAG 51
>gnl|CDD|214708 smart00523, DWA, Domain A in dwarfin family proteins.
Length = 109
Score = 51.6 bits (124), Expect = 4e-10
Identities = 24/55 (43%), Positives = 37/55 (67%), Gaps = 2/55 (3%)
Query: 23 GEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQ-DPNTKCVTIPRLQFEDLQQSG 76
E+K+++KA +SL+KKLKK L+EL +A+ ++ P T+CV IPR LQ +
Sbjct: 1 VEEKWAKKATESLLKKLKK-KQLEELLQAVESKGGPPTRCVLIPRSLDGRLQVAH 54
>gnl|CDD|199816 cd10492, MH1_SMAD_4, N-terminal Mad Homology 1 (MH1) domain in
SMAD4. The MH1 is a small DNA-binding domain present
in SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. MH1 binds to the DNA major groove
in an unusual manner via a beta hairpin structure. It
negatively regulates the functions of the MH2 domain,
the C-terminal domain of SMAD. This MH1 belongs to
SMAD4, a common mediator SMAD (co-SMAD), which belongs
to the Dwarfin family of proteins and is involved in
many cell functions such as differentiation, apoptosis,
gastrulation, embryonic development and cell cycle.
SMAD4 binds receptor regulated SMADs (R-SMADs) such as
SMAD1 or SMAD2, and forms an oligomeric complex that
binds to DNA and serves as a transcription factor.
SMAD4 is often mutated in several cancers, such as
multiploid colorectal cancer and pancreatic carcinoma,
as well as in juvenile polyposis syndrome (JPS).
Length = 125
Score = 48.6 bits (116), Expect = 7e-09
Identities = 25/58 (43%), Positives = 39/58 (67%), Gaps = 2/58 (3%)
Query: 11 IVKKLLGWKKGDGEDKYSEKAVKSLVKKLK-KSNGLDELEKAITTQDPN-TKCVTIPR 66
IV L+ ++G + ++++A++SLVKKLK K + LD L AIT+ + +KCVTI R
Sbjct: 6 IVHSLMCHRQGGESESFAKRAIESLVKKLKDKRDELDSLITAITSNGAHPSKCVTIQR 63
>gnl|CDD|233707 TIGR02071, PBP_1b, penicillin-binding protein 1B. Bacterial that
synthesize a cell wall of peptidoglycan (murein)
generally have several transglycosylases and
transpeptidases for the task. This family consists of a
particular bifunctional transglycosylase/transpeptidase
in E. coli and other Proteobacteria, designated
penicillin-binding protein 1B [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 730
Score = 29.3 bits (66), Expect = 0.22
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 27 YSEKAVKSLVKKLKKSNGLDELEKAITTQDPNT 59
+E+AV+ + LKK L +LE A+ D T
Sbjct: 383 AAEQAVQETIPALKKKKKLPDLEAAMVVTDRFT 415
>gnl|CDD|224287 COG1368, MdoB, Phosphoglycerol transferase and related proteins,
alkaline phosphatase superfamily [Cell envelope
biogenesis, outer membrane].
Length = 650
Score = 28.2 bits (63), Expect = 0.58
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 1 MTSLFPFTPPIVKKLLGWKKGDGED----------KYSEKAVKSLVKKLKKSNGLDE 47
+++ PF P K+ ++ Y+++A+ + KLKKS
Sbjct: 426 LSNHGPFELPEGKRNELLEEPLSASTALANYLQAVHYADEALGQFIDKLKKSGLYKN 482
>gnl|CDD|225766 COG3225, GldG, ABC-type uncharacterized transport system involved
in gliding motility, auxiliary component [Cell motility
and secretion].
Length = 538
Score = 27.9 bits (62), Expect = 0.73
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 7/69 (10%)
Query: 6 PFTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIP 65
PF P+ +K L + + ++ LV+ L S L E++ Q P
Sbjct: 151 PFVRPLEEKFLEYDLARLVIELGQR--TQLVQGLMSSEPLSEIQLTNANQQE-----IRP 203
Query: 66 RLQFEDLQQ 74
R L Q
Sbjct: 204 RAFMVYLLQ 212
>gnl|CDD|217789 pfam03915, AIP3, Actin interacting protein 3.
Length = 424
Score = 26.9 bits (60), Expect = 1.4
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 29 EKAVKSLV--KKLKKSNGLDELEKAITTQD 56
EK + + V KLKKS G++E+E+ +D
Sbjct: 394 EKELGNFVEEGKLKKSGGIEEVERLRKAKD 423
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 26.7 bits (59), Expect = 1.6
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 28 SEKAVKSLVKKLKKSNGLDELEKAITTQD 56
+EKAV+ + LKK L +LE A+ D
Sbjct: 448 AEKAVEEGIPALKKQRKLSDLETAMVVVD 476
>gnl|CDD|214523 smart00119, HECTc, Domain Homologous to E6-AP Carboxyl Terminus
with. E3 ubiquitin-protein ligases. Can bind to E2
enzymes.
Length = 328
Score = 26.8 bits (60), Expect = 1.7
Identities = 16/65 (24%), Positives = 24/65 (36%), Gaps = 5/65 (7%)
Query: 5 FPFTPPIVKKLLGWKKGDGEDKYSEKAV--KSLVKKLKKSNGLDELEKAITTQDPNT--K 60
F P KKLLG K D S KSL L ++ +EL+ + + +
Sbjct: 87 LFFARPFYKKLLG-KPVTLHDLESLDPELYKSLKWLLLNNDTSEELDLTFSIVLTSEFGQ 145
Query: 61 CVTIP 65
+
Sbjct: 146 VKVVE 150
>gnl|CDD|214826 smart00806, AIP3, Actin interacting protein 3. Aip3p/Bud6p is a
regulator of cell and cytoskeletal polarity in
Saccharomyces cerevisiae that was previously identified
as an actin-interacting protein. Actin-interacting
protein 3 (Aip3p) localizes at the cell cortex where
cytoskeleton assembly must be achieved to execute
polarized cell growth, and deletion of AIP3 causes gross
defects in cell and cytoskeletal polarity. Aip3p
localization is mediated by the secretory pathway,
mutations in early- or late-acting components of the
secretory apparatus lead to Aip3p mislocalization.
Length = 426
Score = 26.6 bits (59), Expect = 1.7
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 29 EKAVKSLV--KKLKKSNGLDELEKAITTQD 56
EK + + V KLKKS G++E+E+ +D
Sbjct: 396 EKELGNFVENGKLKKSGGIEEVERLRKAKD 425
>gnl|CDD|238101 cd00172, SERPIN, SERine Proteinase INhibitors (serpins) exhibit
conformational polymorphism shifting from native to
cleaved, latent, delta, or polymorphic forms. Many
serpins, such as antitrypsin and antichymotrypsin,
function as serine protease inhibitors which regulate
blood coagulation cascades. Non-inhibitory serpins
perform many diverse functions such as chaperoning
proteins or transporting hormones. Serpins are of
medical interest because mutants have been associated
with blood clotting disorders, emphysema, cirrhosis, and
dementia.
Length = 364
Score = 26.4 bits (59), Expect = 1.9
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 16/54 (29%)
Query: 40 KKSNGLDELEKAITTQD--------PNTKC-VTIPRLQFED-------LQQSGV 77
K+ GL ELE+ ++ + + VT+P+ + E LQ G+
Sbjct: 229 KEVTGLAELEEKLSAEKLDDLLSNLKEREVEVTLPKFKIESSLDLKEVLQALGI 282
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 26.6 bits (59), Expect = 2.1
Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 23 GEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIPRLQFEDLQQSGV 77
E + + + + KK++ + L+++ K I+ D V I L E L++ G+
Sbjct: 105 DEYEKDREKAEEVAKKIEATK-LEDVAKDISI-DLADMTVII-ELDEEQLKERGI 156
>gnl|CDD|130973 TIGR01918, various_sel_PB, selenoprotein B,
glycine/betaine/sarcosine/D-proline reductase family.
This model represents selenoprotein B of glycine
reductase, sarcosine reductase, betaine reductase,
D-proline reductase, and perhaps others. This model is
built in fragment mode to assist in recognizing
fragmentary translations. All members are expected to
contain an internal TGA codon, encoding selenocysteine,
which may be misinterpreted as a stop codon.
Length = 431
Score = 26.4 bits (58), Expect = 2.2
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 13 KKLLGWKKGDGEDKYSEKAVKSLVKKLK 40
K++ ++ ED+ SE+AV LVKKLK
Sbjct: 173 KRVNHFR----EDRGSERAVDMLVKKLK 196
>gnl|CDD|223693 COG0620, MetE, Methionine synthase II (cobalamin-independent)
[Amino acid transport and metabolism].
Length = 330
Score = 26.1 bits (58), Expect = 2.8
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 5 FPFTPPIVKKLLGWKKGD-GEDKYSEK---AVKSLVKKLKKSNGLDEL 48
FP + K WKKG+ E++Y E A++ +K +++ GLD L
Sbjct: 13 FPRPEELRKAREKWKKGEISEEEYEEILREAIRRAIKDQEEA-GLDVL 59
>gnl|CDD|237582 PRK14011, PRK14011, prefoldin subunit alpha; Provisional.
Length = 144
Score = 25.5 bits (56), Expect = 3.4
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 21 GDGEDKYSEKAVKSLVKKLKKSNGLDELEKA 51
G G D Y EK V +++ KKS ++EL+K
Sbjct: 75 GVGSDIYLEKDVSEVIEDFKKS--VEELDKT 103
>gnl|CDD|132035 TIGR02990, ectoine_eutA, ectoine utilization protein EutA. Members
of this protein family are EutA, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti and Silicibacter pomeroyi.
It is missing from two other species with the other
ectoine transport and utilization genes: Pseudomonas
putida and Agrobacterium tumefaciens.
Length = 239
Score = 25.7 bits (56), Expect = 3.7
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 44 GLDELEKAITTQDPNTKCVTIPRLQFEDLQQSGV 77
G DE+ +AI P T VT + L GV
Sbjct: 87 GDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGV 120
>gnl|CDD|185747 cd09234, V_HD-PTP_like, Protein-interacting V-domain of mammalian
His-Domain type N23 protein tyrosine phosphatase and
related domains. This family contains the V-shaped (V)
domain of mammalian His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23) and related
domains. It belongs to the V_Alix_like superfamily which
includes the V domains of Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, mammalian Alix
(apoptosis-linked gene-2 interacting protein X/ also
known as apoptosis-linked gene-2 interacting protein 1,
AIP1), and related domains. HD_PTP interacts with the
ESCRT (Endosomal Sorting Complexes Required for
Transport) system, and participates in cell migration
and endosomal trafficking. The related Alix V-domain
(belonging to a different family in this superfamily)
contains a binding site, partially conserved in the
superfamily, for the retroviral late assembly (L) domain
YPXnL motif. The Alix V-domain is also a dimerization
domain. In addition to the V-domain, HD_PTP also has an
N-terminal Bro1-like domain, a proline-rich region
(PRR), a catalytically inactive tyrosine phosphatase
domain, and a region containing a PEST motif. Bro1-like
domains bind components of the ESCRT-III complex,
specifically to CHMP4 in the case of HD-PTP. The
Bro1-like domain of HD-PTP can also bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
HD-PTP is encoded by the PTPN23 gene, a tumor suppressor
gene candidate frequently absent in human kidney,
breast, lung, and cervical tumors. This family also
contains Drosophila Myopic, which promotes epidermal
growth factor receptor (EGFR) signaling, and
Caenorhabditis elegans (enhancer of glp-1) EGO-2 which
promotes Notch signaling.
Length = 337
Score = 25.7 bits (57), Expect = 4.2
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 38 KLKKSNGLDELEKAITTQDPNTKCVTIPRLQFEDLQQS 75
K +SN EL KA+ N K + P ++LQ+
Sbjct: 142 KASQSN--TELHKAMNLHIANLKLLAGP---LDELQKK 174
>gnl|CDD|203622 pfam07355, GRDB, Glycine/sarcosine/betaine reductase selenoprotein
B (GRDB). This family represents a conserved region
approximately 350 residues long within the selenoprotein
B component of the bacterial glycine, sarcosine and
betaine reductase complexes.
Length = 349
Score = 25.4 bits (56), Expect = 4.9
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 24 EDKYSEKAVKSLVKKLK 40
E++ +++AV LVKKLK
Sbjct: 184 EERGAKRAVDMLVKKLK 200
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 25.3 bits (56), Expect = 5.0
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNGL 45
K + + V+ LVKKL+K GL
Sbjct: 82 PDGKKKTFEDVEELVKKLEKEWGL 105
>gnl|CDD|165168 PHA02818, PHA02818, hypothetical protein; Provisional.
Length = 92
Score = 24.5 bits (53), Expect = 5.6
Identities = 8/23 (34%), Positives = 18/23 (78%)
Query: 19 KKGDGEDKYSEKAVKSLVKKLKK 41
K D E+KY+EK ++ ++++++K
Sbjct: 10 KSIDNENKYNEKFIECIIQEIEK 32
>gnl|CDD|187786 cd09655, CasRa_I-A, CRISPR/Cas system-associated transcriptional
regulator CasRa. 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; Predicted transcriptional regulator of
CRISPR/Cas system.
Length = 198
Score = 25.0 bits (55), Expect = 6.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 25 DKYSEKAVKSLVKKLKKSNG-----LDELEK 50
EK+VK++ KKL KS L ELEK
Sbjct: 149 KAKGEKSVKNIAKKLGKSLSTISRHLRELEK 179
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 25.0 bits (55), Expect = 6.1
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 5 FPFTPPIVKKLLGWKKGDGEDKYS--EKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCV 62
PF P KKLLG K ED + +SL L+ +EL T +
Sbjct: 60 LPFPPAFWKKLLG-KPITLEDLEEVDPELYRSLKSLLELDGDEEELCLTFTVSGEGEGTI 118
>gnl|CDD|236488 PRK09374, rplB, 50S ribosomal protein L2; Validated.
Length = 276
Score = 25.0 bits (56), Expect = 6.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNG 44
D + K KSL++ LKKS G
Sbjct: 20 DFSELTKGKPEKSLLEPLKKSGG 42
>gnl|CDD|226730 COG4280, COG4280, Predicted membrane protein [Function unknown].
Length = 236
Score = 25.2 bits (55), Expect = 6.2
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 11 IVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQ 55
V++ G +KG GE+K E V ++ G +L + +
Sbjct: 85 AVRRFAGIRKGGGEEKLEEGIVLD-----QEEEGFSKLALLVVFK 124
>gnl|CDD|185563 PTZ00337, PTZ00337, surface protease GP63; Provisional.
Length = 567
Score = 25.2 bits (55), Expect = 6.4
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 57 PNTKCVTIPRLQFEDLQQSGVC 78
PN++CV LQF+D VC
Sbjct: 454 PNSRCVKGQDLQFDDEYIGDVC 475
>gnl|CDD|215699 pfam00079, Serpin, Serpin (serine protease inhibitor). Structure
is a multi-domain fold containing a bundle of helices
and a beta sandwich.
Length = 369
Score = 24.9 bits (55), Expect = 6.7
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 40 KKSNGLDELEKAITTQD-----------PNTKCVTIPRLQFE 70
+ GL+ELEK++T + + + +P+ + E
Sbjct: 229 DEGGGLEELEKSLTAELLEEWLSSLKPRKVREELYLPKFKIE 270
>gnl|CDD|220535 pfam10037, MRP-S27, Mitochondrial 28S ribosomal protein S27.
Members of this family of small ribosomal proteins
possess one of three conserved blocks of sequence found
in proteins that stimulate the dissociation of guanine
nucleotides from G-proteins, leaving open the
possibility that MRP-S27 might be a functional partner
of GTP-binding ribosomal proteins.
Length = 417
Score = 25.1 bits (55), Expect = 6.9
Identities = 12/51 (23%), Positives = 20/51 (39%)
Query: 6 PFTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQD 56
I++KL K E KS +L + L+E+EK+ +
Sbjct: 283 DLLQSILEKLSSELDEASLKKLQEAIDKSESSELDEDLLLEEVEKSKQKFE 333
>gnl|CDD|223969 COG1039, RnhC, Ribonuclease HIII [DNA replication, recombination,
and repair].
Length = 297
Score = 24.6 bits (54), Expect = 8.5
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 26 KYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTK 60
K + AV ++ + G +LE+ N +
Sbjct: 257 KGAGPAVDQAAAEIIQKRGFSKLEQVAKLHFKNFQ 291
>gnl|CDD|213341 cd05392, RasGAP_Neurofibromin_like, Ras-GTPase Activating Domain of
proteins similar to neurofibromin. Neurofibromin-like
proteins include the Saccharomyces cerevisiae RasGAP
proteins Ira1 and Ira2, the closest homolog of
neurofibromin, which is responsible for the human
autosomal dominant disease neurofibromatosis type I
(NF1). The RasGAP Ira1/2 proteins are negative
regulators of the Ras-cAMP signaling pathway and
conserved from yeast to human. In yeast Ras proteins are
activated by GEFs, and inhibited by two GAPs, Ira1 and
Ira2. Ras proteins activate the cAMP/protein kinase A
(PKA) pathway, which controls metabolism, stress
resistance, growth, and meiosis. Recent studies showed
that the kelch proteins Gpb1 and Gpb2 inhibit Ras
activity via association with Ira1 and Ira2. Gpb1/2 bind
to a conserved C-terminal domain of Ira1/2, and loss of
Gpb1/2 results in a destabilization of Ira1 and Ira2,
leading to elevated levels of Ras2-GTP and uninhibited
cAMP-PKA signaling. Since the Gpb1/2 binding domain on
Ira1/2 is conserved in the human neurofibromin protein,
the studies suggest that an analogous signaling
mechanism may contribute to the neoplastic development
of NF1.
Length = 317
Score = 24.6 bits (54), Expect = 8.6
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 26 KYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTK 60
KY K ++ L+ ++ + E+EK I D N +
Sbjct: 91 KYLRKVLRPLLTEIVDNKDYFEVEK-IKPDDENLE 124
>gnl|CDD|151710 pfam11269, DUF3069, Protein of unknown function (DUF3069). This
family of proteins with unknown function appear to be
restricted to Gammaproteobacteria.
Length = 121
Score = 24.3 bits (53), Expect = 9.3
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 25 DKYSEKAVKSLVKKLKKS 42
D+ +K VK+LKK+
Sbjct: 89 DRVLHNCLKDSVKQLKKA 106
>gnl|CDD|111185 pfam02263, GBP, Guanylate-binding protein, N-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 264
Score = 24.7 bits (54), Expect = 9.5
Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 8/60 (13%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTKCVTIPR--------LQFEDLQ 73
D+Y E +K + ++ + + I + P KC R Q E L+
Sbjct: 177 ITGDEYLENRLKLSQGQHEELQNFNLPRECIRSFFPKRKCFLFDRPGLDVALNPQLEGLR 236
>gnl|CDD|182148 PRK09922, PRK09922,
UDP-D-galactose:(glucosyl)lipopolysaccharide-1,
6-D-galactosyltransferase; Provisional.
Length = 359
Score = 24.7 bits (54), Expect = 9.7
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNGLDELEKAI 52
GE KY A+ + +++ + L A+
Sbjct: 323 SGEVKYQHDAIPNSIERFYEVLYFKNLNNAL 353
>gnl|CDD|240292 PTZ00148, PTZ00148, 40S ribosomal protein S8; Provisional.
Length = 205
Score = 24.6 bits (54), Expect = 9.7
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 19 KKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQ 55
K + E+K ++K +SLV KL+ +++KA+ Q
Sbjct: 127 YKKEEENKKAKKKSESLVAKLEVRKKNHKIDKALLEQ 163
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 0.389
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,504,138
Number of extensions: 345060
Number of successful extensions: 413
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 46
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
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)