RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11911
(279 letters)
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 32.2 bits (74), Expect = 0.26
Identities = 24/104 (23%), Positives = 38/104 (36%), Gaps = 23/104 (22%)
Query: 77 AWLNIVQQRVPNLSAMTCSDYKQYESLFKALDEDMKVHLVRTTQLVSVCRSITNLIDCPH 136
AW +IV +PN+ + + + D V R T LV + S +
Sbjct: 164 AWSSIVYSLIPNIQVLE----SNLKKFADICEADEVVLFERATFLV-ISHSSRK--EASA 216
Query: 137 LEPATESHRFE------------ILNLERSISSGLIKLSTFTEY 168
L+P HRFE L+ S S ++ S F+ +
Sbjct: 217 LDP----HRFEKISNIIKQFKLSCSKLQASFQSMEVRNSNFSAF 256
>gnl|CDD|218897 pfam06100, Strep_67kDa_ant, Streptococcal 67 kDa
myosin-cross-reactive antigen like family. Members of
this family are thought to have structural features in
common with the beta chain of the class II antigens, as
well as myosin, and may play an important role in the
pathogenesis.
Length = 500
Score = 32.0 bits (73), Expect = 0.31
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 85 RVPNLSAMTCSDYKQYESLFKALDEDMKVHLVR 117
+P+ SA+ + Y QYESL + + +K H V
Sbjct: 191 GLPDFSALKFTKYNQYESLVLPMIKYLKSHGVD 223
>gnl|CDD|206142 pfam13972, TetR, Bacterial transcriptional repressor. This family
of bacterial transcriptional repressors is characterized
by the short approximately 50 amino acid stretch of
residues constituting the helix-turn-helix DNA binding
motif, around the YRFhY motif. The target proteins that
are repressed are involved in the transcriptional
control of multi-drug efflux pumps, pathways for the
biosynthesis of antibiotics, response to osmotic stress
and toxic chemicals, control of catabolic pathways,
differentiation processes, and pathogenicity. The
regulatory network in which TetR itself is involved is
in being released in the presence of tetracycline,
binding to the target operator, and repressing tetA
transcription.
Length = 146
Score = 29.9 bits (68), Expect = 0.72
Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 21/90 (23%)
Query: 1 MQKYRTFFMNLSHCRSLLESLESHLDPATRNKFSELHKQLHQQACDIL-----------D 49
M +YR + +L LL DP + ++ +L ++L + IL D
Sbjct: 35 MWRYRFLYRDLPD---LLSR-----DPELKRRYRQLQQRLLEALRAILEGLREAGILRID 86
Query: 50 KAAIRS--QQMALAASKWISLDQNLHEEAA 77
+ + + L + W+S + L AA
Sbjct: 87 DEELDALADNIWLVLTFWLSFLRTLSPRAA 116
>gnl|CDD|221797 pfam12830, Nipped-B_C, Sister chromatid cohesion C-terminus. This
domain lies towards the C-terminus of nipped-B or sister
chromatid cohesion proteins.
Length = 187
Score = 30.0 bits (68), Expect = 0.97
Identities = 15/63 (23%), Positives = 29/63 (46%)
Query: 8 FMNLSHCRSLLESLESHLDPATRNKFSELHKQLHQQACDILDKAAIRSQQMALAASKWIS 67
+N C L +LE+ +P R+ L K+LH++ ++D ++A + +S
Sbjct: 40 LVNPKECVPTLIALETDPNPLIRSLALALLKELHEKHESLVDSRYSEGVKLAFDYQRRLS 99
Query: 68 LDQ 70
D
Sbjct: 100 SDP 102
>gnl|CDD|227060 COG4716, COG4716, Myosin-crossreactive antigen [Function unknown].
Length = 587
Score = 30.6 bits (69), Expect = 0.98
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 85 RVPNLSAMTCSDYKQYESLFKALDEDMKVHLV 116
+P+ SA+ + Y QYESL L +K H V
Sbjct: 211 GLPDFSALKFTKYNQYESLVLPLITYLKSHGV 242
>gnl|CDD|203610 pfam07311, Dodecin, Dodecin. Dodecin is a flavin-binding
protein,found in several bacteria and few archaea and
represents a stand-alone version of the SHS2 domain. It
most closely resembles the SHS2 domains of FtsA and
Rpb7p, and represents a single domain small-molecule
binding form.
Length = 66
Score = 27.1 bits (61), Expect = 2.6
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 180 ESWMDAHQNQIESLNKS-NNMKSYW--ELKAQIE 210
ESW DA QN IE +K+ N++ + E + +E
Sbjct: 14 ESWEDAIQNAIERASKTLRNLRWFEVKETRGHVE 47
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon
Stimulated Gene product of 20 kDa, and similar proteins.
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20) is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. It was also
independently identified by its response to estrogen and
was called HEM45 (human estrogen regulated transcript).
ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease
containing three conserved sequence motifs termed ExoI,
ExoII and ExoIII with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. ISG20 may be a major effector of innate
immunity against pathogens including viruses, bacteria,
and parasites. It is located in promyelocytic leukemia
(PML) nuclear bodies, sites for oncogenic DNA viral
transcription and replication. It may carry out its
function by degrading viral RNAs as part of the
IFN-regulated antiviral response.
Length = 157
Score = 28.6 bits (64), Expect = 2.7
Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 4/56 (7%)
Query: 104 FKALDEDMKVHLVRTTQLVSVCRSITNLIDCPHLEPATESHRFEILNLERSISSGL 159
FKAL H+ R T S + P + + L L R I G
Sbjct: 89 FKALKYFHPKHMTRDT---STIPLLNRKAGFPENCRVSLKVLAKRL-LHRDIQVGR 140
>gnl|CDD|205311 pfam13130, DUF3952, Domain of unknown function (DUF3952). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
110 amino acids in length. There is a conserved VMSAS
sequence motif.
Length = 107
Score = 27.4 bits (61), Expect = 3.6
Identities = 11/14 (78%), Positives = 11/14 (78%), Gaps = 1/14 (7%)
Query: 100 YESLFKALDE-DMK 112
YE L KALDE DMK
Sbjct: 16 YERLVKALDEGDMK 29
>gnl|CDD|153365 cd07681, F-BAR_PACSIN3, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 3 (PACSIN3). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 3 or Syndapin III is expressed ubiquitously and
regulates glucose uptake in adipocytes through its role
in GLUT1 trafficking. It also modulates the subcellular
localization and stimulus-specific function of the
cation channel TRPV4. PACSIN 3 contains an N-terminal
F-BAR domain and a C-terminal SH3 domain. F-BAR domains
form banana-shaped dimers with a positively-charged
concave surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 258
Score = 28.4 bits (63), Expect = 3.7
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 11 LSHCRSLLESLESHLDPATRNKFSELHKQLHQ 42
L + +L L HLD ++ + F L++ LHQ
Sbjct: 224 LCFFKEMLLDLHQHLDLSSSDSFHALYRDLHQ 255
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent) systems
that are largely represented in archaea and eubacteria
and are primarily involved in scavenging solutes from
the environment. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 178
Score = 27.9 bits (63), Expect = 4.0
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 23 SHLDPATRNKFSELHKQLHQQ 43
S LDP TR + L K L Q
Sbjct: 129 SALDPITRREVRALLKSLQAQ 149
>gnl|CDD|204699 pfam11646, DUF3258, Protein of unknown function DUF3258. This
viral family are possible phage integrase proteins
however this cannot be confirmed.
Length = 111
Score = 27.2 bits (60), Expect = 4.3
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 88 NLSAMTCSDYKQYESLFKALDEDMKVHLVRTTQL---VSVCRSITNLIDCPHLEP 139
L + DY ++E ++ A+D D K+ + + + I ID P+ P
Sbjct: 21 GLYVLKQKDYARFEIVWVAIDPDGKIEERTVYSIETYWYIFKDIGIFIDRPYELP 75
>gnl|CDD|222707 pfam14357, DUF4404, Domain of unknown function (DUF4404). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 90 amino acids in
length. There are two completely conserved residues (P
and G) that may be functionally important.
Length = 85
Score = 26.4 bits (59), Expect = 5.5
Identities = 13/35 (37%), Positives = 14/35 (40%), Gaps = 6/35 (17%)
Query: 15 RSLLESLESHL------DPATRNKFSELHKQLHQQ 43
R LLE L L D TR SEL + Q
Sbjct: 3 RELLEQLHEELEQTDSLDEETRALLSELIDDIEAQ 37
>gnl|CDD|198372 cd07804, FGGY_XK_like_1, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
bacterial and archaeal xylulose kinases-like proteins
with similarity to bacterial D-xylulose kinases (XK,
also known as xylulokinase; EC 2.7.1.17), which catalyze
the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 492
Score = 27.9 bits (63), Expect = 6.7
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 59 ALAASKWISLDQNLHEEAAWLNIVQQRVPNLSAMTCSD--YKQYESLFKALDEDM 111
AL A+ + + +L E AW+ + + P+ D Y+ Y L+ AL E M
Sbjct: 438 ALLAAVAVGVYDDLEEVKAWVKVRETIEPDPENHEIYDEYYEIYRELYPALKELM 492
>gnl|CDD|185750 cd09237, V_ScBro1_like, Protein-interacting V-domain of
Saccharomyces cerevisiae Bro1 and related domains. This
family contains the V-shaped (V) domain of Saccharomyces
cerevisiae Bro1, and related domains. It belongs to the
V_Alix_like superfamily which also includes the V-domain
of Saccharomyces cerevisiae Rim20 (also known as PalA),
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Bro1 interacts with the ESCRT (Endosomal
Sorting Complexes Required for Transport) system, and
participates in endosomal trafficking. The mammalian
Alix V-domain (belonging to a different family) 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. Bro1
also has an N-terminal Bro1-like domain, which binds
Snf7, a component of the ESCRT-III complex, and a
C-terminal proline-rich region (PRR). The C-terminal
portion (V-domain and PRR) of S. cerevisiae Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes. It interacts with a
YPxL motif in the Doa4s catalytic domain to stimulate
its deubiquitination activity.
Length = 356
Score = 27.3 bits (61), Expect = 8.8
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 180 ESWMDAHQNQIESLNKS-NNMKSYWE-LKAQIEFYNTLLDRSRD 221
+S + E L K+ N+ K + L +EFY+ LL ++D
Sbjct: 301 KSKQKLRKEFFEKLKKAYNSFKKFSAGLPKGLEFYDDLLKMAKD 344
>gnl|CDD|199875 cd06905, M14-like_8, Peptidase M14-like domain; uncharacterized
subfamily. A functionally uncharacterized subgroup of
the M14 family of metallocarboxypeptidases (MCPs). The
M14 family are zinc-binding carboxypeptidases (CPs)
which hydrolyze single, C-terminal amino acids from
polypeptide chains, and have a recognition site for the
free C-terminal carboxyl group, which is a key
determinant of specificity. Two major subfamilies of the
M14 family, defined based on sequence and structural
homology, are the A/B and N/E subfamilies. Enzymes
belonging to the A/B subfamily are normally synthesized
as inactive precursors containing preceding signal
peptide, followed by an N-terminal pro-region linked to
the enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 360
Score = 27.4 bits (61), Expect = 9.2
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 165 FTEYWLEYQTLADRLESWMDAHQNQI--ESLNKSNNMKSYWELKAQIEFYNTLLDRSRDN 222
F Y Y L L++W A+ + I ES+ KS + W L + T R +
Sbjct: 1 FDRY-YRYDELTAFLQAWASAYPHLISLESIGKSYEGRDIWLLT--LTNQATGPAREKPA 57
Query: 223 F 223
F
Sbjct: 58 F 58
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 27.5 bits (61), Expect = 9.2
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 4/22 (18%)
Query: 14 CRSLLESLESHLDPATRNKFSE 35
CR+++E+L SHL NK+SE
Sbjct: 161 CRAVMEALGSHLT----NKYSE 178
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 27.6 bits (62), Expect = 9.7
Identities = 9/52 (17%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 175 LADRLESWMDAHQNQIESLNKSNNMKSYWELKAQIEFYNTLLDR--SRDNFE 224
D+L W +++ + I N+ N + ++ + L D +R + +
Sbjct: 197 FQDKLLEWYESNPDFIWPANRRNEVLNFLK--------EGLKDLSITRTDLD 240
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
0.319 0.130 0.385
Gapped
Lambda K H
0.267 0.0719 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,723,460
Number of extensions: 1249026
Number of successful extensions: 1345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1340
Number of HSP's successfully gapped: 45
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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 (21.8 bits)
S2: 58 (26.1 bits)