RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7307
(117 letters)
>gnl|CDD|238113 cd00190, Tryp_SPc, Trypsin-like serine protease; Many of these are
synthesized as inactive precursor zymogens that are
cleaved during limited proteolysis to generate their
active forms. Alignment contains also inactive enzymes
that have substitutions of the catalytic triad residues.
Length = 232
Score = 69.2 bits (170), Expect = 2e-15
Identities = 24/50 (48%), Positives = 32/50 (64%), Gaps = 3/50 (6%)
Query: 34 GDSGGPLLLQRPDKQWTIIGVVSWGIGCGK--TPGVYVQVNKYLRWIYNT 81
GDSGGPL+ + ++G+VSWG GC + PGVY +V+ YL WI T
Sbjct: 184 GDSGGPLVCNDNG-RGVLVGIVSWGSGCARPNYPGVYTRVSSYLDWIQKT 232
Score = 52.3 bits (126), Expect = 3e-09
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 83 KGDSGGPLLLQRPDKQWTIIGVVSWGIGCAQ 113
+GDSGGPL+ + ++G+VSWG GCA+
Sbjct: 183 QGDSGGPLVCNDNG-RGVLVGIVSWGSGCAR 212
>gnl|CDD|214473 smart00020, Tryp_SPc, Trypsin-like serine protease. Many of these
are synthesised as inactive precursor zymogens that are
cleaved during limited proteolysis to generate their
active forms. A few, however, are active as single chain
molecules, and others are inactive due to substitutions
of the catalytic triad residues.
Length = 229
Score = 67.3 bits (165), Expect = 8e-15
Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 4/47 (8%)
Query: 34 GDSGGPLLLQRPDKQWTIIGVVSWGIGCGKT--PGVYVQVNKYLRWI 78
GDSGGPL+ D +W ++G+VSWG GC + PGVY +V+ YL WI
Sbjct: 185 GDSGGPLVCN--DGRWVLVGIVSWGSGCARPGKPGVYTRVSSYLDWI 229
Score = 52.3 bits (126), Expect = 3e-09
Identities = 17/33 (51%), Positives = 24/33 (72%), Gaps = 2/33 (6%)
Query: 81 TAKGDSGGPLLLQRPDKQWTIIGVVSWGIGCAQ 113
+GDSGGPL+ D +W ++G+VSWG GCA+
Sbjct: 182 ACQGDSGGPLVCN--DGRWVLVGIVSWGSGCAR 212
>gnl|CDD|215708 pfam00089, Trypsin, Trypsin.
Length = 218
Score = 51.3 bits (123), Expect = 6e-09
Identities = 26/47 (55%), Positives = 30/47 (63%), Gaps = 6/47 (12%)
Query: 34 GDSGGPLLLQRPDKQWTIIGVVSWGIGC--GKTPGVYVQVNKYLRWI 78
GDSGGPL+ D +IG+VSWG GC G PGVY V+ YL WI
Sbjct: 176 GDSGGPLV--CSDG--ELIGIVSWGYGCASGNYPGVYTPVSSYLDWI 218
Score = 37.0 bits (86), Expect = 7e-04
Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 4/33 (12%)
Query: 81 TAKGDSGGPLLLQRPDKQWTIIGVVSWGIGCAQ 113
+GDSGGPL+ D +IG+VSWG GCA
Sbjct: 173 ACQGDSGGPLV--CSDG--ELIGIVSWGYGCAS 201
>gnl|CDD|227927 COG5640, COG5640, Secreted trypsin-like serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 413
Score = 46.0 bits (109), Expect = 6e-07
Identities = 27/58 (46%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 26 RTSRQAQTGDSGGPLLLQRPD--KQWTIIGVVSWGIG-CGKT--PGVYVQVNKYLRWI 78
R + A GDSGGP+ + + Q GVVSWG G CG T PGVY V+ Y WI
Sbjct: 220 RPPKDACQGDSGGPIFHKGEEGRVQ---RGVVSWGDGGCGGTLIPGVYTNVSNYQDWI 274
Score = 28.7 bits (64), Expect = 0.58
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 79 YNTAKGDSGGPLLLQRPD--KQWTIIGVVSWGIG-CA 112
+ +GDSGGP+ + + Q GVVSWG G C
Sbjct: 223 KDACQGDSGGPIFHKGEEGRVQ---RGVVSWGDGGCG 256
>gnl|CDD|217015 pfam02395, Peptidase_S6, Immunoglobulin A1 protease. This family
consists of immunoglobulin A1 protease proteins. The
immunoglobulin A1 protease cleaves immunoglobulin IgA
and is found in pathogenic bacteria such as Neisseria
gonorrhoeae. Not all of the members of this family are
IgA proteases, espP from E. coli O157:H7 cleaves human
coagulation factor V and hbp is a hemoglobin protease
from E. coli EB1.
Length = 758
Score = 32.1 bits (73), Expect = 0.047
Identities = 29/106 (27%), Positives = 39/106 (36%), Gaps = 12/106 (11%)
Query: 15 QLVRADYDVFNRTSRQAQ-TGDSGGPLLLQRPDK-QWTIIGVVSWGIGCG-------KTP 65
+ Y VF R Q D G + ++ G VS+ IG G
Sbjct: 130 YQDKERYPVFVRLGSGRQYIKDKNGNGVKVVSGAYRYLTAGTVSYLIGLGNGSMIHSGDL 189
Query: 66 GVYVQVNKYLRWIYNTAKGDSGGPLLL-QRPDKQWTIIGVVSWGIG 110
G N L Y + GDSG PL K+W ++GV+ G G
Sbjct: 190 GQTYSQNGPLP-NY-GSLGDSGSPLFAYDNQKKKWVLLGVLDGGAG 233
Score = 30.2 bits (68), Expect = 0.24
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 34 GDSGGPLLL-QRPDKQWTIIGVVSWGIGCGKTPG 66
GDSG PL K+W ++GV+ G G G
Sbjct: 206 GDSGSPLFAYDNQKKKWVLLGVLDGGAGYGGKGN 239
>gnl|CDD|200501 cd11240, Sema_4, The Sema domain, a protein interacting module, of
class 4 semaphorins (Sema4). Class 4 semaphorins
(Sema4s) are transmembrane regulator molecules involved
in the development of the nervous system, immune
response, cytoskeletal organization, angiogenesis, and
cell-cell interactions. There are 7 distinct subfamilies
in class 4 semaphorins, named 4A to 4G. Several class 4
subfamilies play important roles in the immune system
and are called "immune semaphorins". Sema4A plays
critical roles in T cell-DC interactions in the immune
response. Sema4D/CD100, expressed by lymphocytes,
promotes the aggregation and survival of B lymphocytes
and inhibits cytokine-induced migration of immune cells
in vitro. It is required for normal activation of B and
T lymphocytes. Sema4B negatively regulates basophil
functions through T cell-basophil contacts and
significantly inhibits IL-4 and IL-6 production from
basophils in response to various stimuli, including IL-3
and papain. Sema4s not only influence the activation
state of cells but also modulate their migration and
survival. The effects of Sema4s on nonlymphoid cells are
mediated by plexin D1 and plexin Bs. The Sema4G and
Sema4C genes are expressed in the developing cerebellar
cortex and are involved in neural tube closure and
development of cerebellar granules cells through
receptor plexin B2. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 29.3 bits (66), Expect = 0.38
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 21 YDVFNRT--SRQAQ--TGDSGGPLLLQRPDKQWT 50
YD + + SR A+ GD GG LQ K+WT
Sbjct: 204 YDFYEKVTVSRVARVCKGDLGGQRTLQ---KKWT 234
>gnl|CDD|163657 cd07414, MPP_PP1_PPKL, PP1, PPKL (PP1 and kelch-like) enzymes, and
related proteins, metallophosphatase domain. PP1
(protein phosphatase type 1) is a serine/threonine
phosphatase that regulates many cellular processes
including: cell-cycle progression, protein synthesis,
muscle contraction, carbohydrate metabolism,
transcription and neuronal signaling, through its
interaction with at least 180 known targeting proteins.
PP1 occurs in all tissues and regulates many pathways,
ranging from cell-cycle progression to carbohydrate
metabolism. Also included here are the PPKL (PP1 and
kelch-like) enzymes including the PPQ, PPZ1, and PPZ2
fungal phosphatases. These PPKLs have a large
N-terminal kelch repeat in addition to a C-terminal
phosphoesterase domain. The PPP (phosphoprotein
phosphatase) family, to which PP1 belongs, is one of two
known protein phosphatase families specific for serine
and threonine. The PPP family also includes: PP2A, PP2B
(calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE,
PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain
is defined by three conserved motifs (-GDXHG-, -GDXVDRG-
and -GNHE-). The PPP enzyme family is ancient with
members found in all eukaryotes, and in most bacterial
and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 293
Score = 27.3 bits (61), Expect = 1.7
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 7 LVLICAAHQLVRADYDVFNRTSRQAQT 33
L LIC AHQ+V Y+ F + RQ T
Sbjct: 234 LDLICRAHQVVEDGYEFFAK--RQLVT 258
>gnl|CDD|176358 cd01760, RBD, Ubiquitin-like domain of RBD-like S/T kinases. The
ras-binding domain (RBD) of the serine/threonine kinase
raf is structurally quite similar to the beta-grasp
fold of ubiquitin. A raf-like RBD is also present in
RGS12 and other members of a family of GTPase
activating proteins and TIAM1, a guanine nucleotide
exchange protein.
Length = 72
Score = 25.6 bits (57), Expect = 2.6
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 1 MSLCLVLVLICAAHQLVRADYDVF 24
MS+ VL C L DVF
Sbjct: 20 MSVRDVLAKACKKRGLNPECCDVF 43
>gnl|CDD|215133 PLN02241, PLN02241, glucose-1-phosphate adenylyltransferase.
Length = 436
Score = 26.4 bits (59), Expect = 3.7
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 8 VLICAAHQLVRADYDVFNRTSRQ 30
VLI + L R DY F + R+
Sbjct: 125 VLILSGDHLYRMDYMDFVQKHRE 147
>gnl|CDD|100014 cd00286, Tubulin_FtsZ, Tubulin/FtsZ: Family includes tubulin
alpha-, beta-, gamma-, delta-, and epsilon-tubulins as
well as FtsZ, all of which are involved in polymer
formation. Tubulin is the major component of
microtubules, but also exists as a heterodimer and as a
curved oligomer. Microtubules exist in all eukaryotic
cells and are responsible for many functions, including
cellular transport, cell motility, and mitosis. FtsZ
forms a ring-shaped septum at the site of bacterial cell
division, which is required for constriction of cell
membrane and cell envelope to yield two daughter cells.
FtsZ can polymerize into tubes, sheets, and rings in
vitro and is ubiquitous in eubacteria, archaea, and
chloroplasts.
Length = 328
Score = 26.6 bits (59), Expect = 3.8
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 7/52 (13%)
Query: 33 TGDSGGPLLLQRPDKQWTIIGVVSWGIGCGKTPGVYVQVNKYLRWIYNTAKG 84
TG GP+L +R ++ +++ I PG V YN+
Sbjct: 102 TGSGLGPVLAERLKDEYPKRLKITFSI----LPGPDEGVIVRP---YNSILT 146
>gnl|CDD|233450 TIGR01528, NMN_trans_PnuC, nicotinamide mononucleotide transporter
PnuC. The PnuC protein of E. coli is membrane protein
responsible for nicotinamide mononucleotide transport,
subject to regulation by interaction with the NadR (also
called NadI) protein (see TIGR01526). This model defines
a region corresponding to most of the length of PnuC,
found primarily in pathogens. The extreme N- and
C-terminal regions are poorly conserved and not included
in the alignment and model [Transport and binding
proteins, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridine nucleotides].
Length = 189
Score = 26.2 bits (58), Expect = 4.3
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 67 VYVQVNKYLRWIYNTAKGDSGGPLLLQRPD-KQWTIIGVVSWGIGCAQVL 115
V + W N+ + ++G L++ K WTII S + L
Sbjct: 57 VIANIYGLFAWKKNSQQEENGVTSGLKKLKGKGWTIILSTSVVLTVVIAL 106
>gnl|CDD|222077 pfam13365, Trypsin_2, Trypsin-like peptidase domain. This family
includes trypsin like peptidase domains.
Length = 138
Score = 25.6 bits (56), Expect = 5.7
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 53 GVVSWGIGCGKTPGVYVQVNKYLRWIYN--TAKGDSGGPLLLQRPDKQWTIIGV 104
G G G G + + + T+ G SGGP+ D ++G+
Sbjct: 89 GASGGGGGVGGLVSGSLGGVDGRYILTDADTSPGSSGGPVF----DADGEVVGI 138
>gnl|CDD|217716 pfam03761, DUF316, Domain of unknown function (DUF316). This
family of proteins with unknown function are from
Caenorhabditis elegans. The protein has GO references
indicating the protein is a positive regulator of growth
rate and is also involved in nematode larval
development.
Length = 280
Score = 25.5 bits (56), Expect = 7.3
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 80 NTAKGDSGGPLLLQRPDKQWTIIGV 104
KGD GGPL+ K T+IG
Sbjct: 225 YLCKGDDGGPLIKNVSGK-NTVIGF 248
>gnl|CDD|163658 cd07415, MPP_PP2A_PP4_PP6, PP2A, PP4, and PP6 phosphoprotein
phosphatases, metallophosphatase domain. PP2A-like
family of phosphoprotein phosphatases (PPP's) including
PP4 and PP6. PP2A (Protein phosphatase 2A) is a
critical regulator of many cellular activities. PP2A
comprises about 1% of total cellular proteins. PP2A,
together with protein phosphatase 1 (PP1), accounts for
more than 90% of all serine/threonine phosphatase
activities in most cells and tissues. The PP2A subunit
in addition to having a catalytic domain homologous to
PP1, has a unique C-terminal tail, containing a motif
that is conserved in the catalytic subunits of all
PP2A-like phosphatases including PP4 and PP6, and has an
important role in PP2A regulation. The PP2A-like family
of phosphatases all share a similar heterotrimeric
architecture, that includes: a 65kDa scaffolding subunit
(A), a 36kDa catalytic subunit (C), and one of 18
regulatory subunits (B). The PPP (phosphoprotein
phosphatase) family, to which PP2A belongs, is one of
two known protein phosphatase families specific for
serine and threonine. The PPP family also includes:
PP1, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC,
PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic
domain is defined by three conserved motifs (-GDXHG-,
-GDXVDRG- and -GNHE-). The PPP enzyme family is ancient
with members found in all eukaryotes, and in most
bacterial and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 285
Score = 25.3 bits (56), Expect = 7.9
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 7 LVLICAAHQLVRADYDV-FNRT 27
L LIC AHQLV Y F+
Sbjct: 226 LTLICRAHQLVMEGYQWMFDDK 247
>gnl|CDD|217684 pfam03710, GlnE, Glutamate-ammonia ligase adenylyltransferase.
Conserved repeated domain found in GlnE proteins. These
proteins adenylate and deadenylate glutamine synthases:
ATP + {L-Glutamate:ammonia ligase (ADP-forming)} =
Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase
(ADP-forming)}. The family is related to the pfam01909
domain.
Length = 251
Score = 25.3 bits (56), Expect = 8.7
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 75 LRWIYNTAKGDSGGPLLLQRPDKQWTIIG 103
L W + + G P LQ + +IG
Sbjct: 105 LDWAWRQVCAEGGTPGHLQGEPQGLAVIG 133
>gnl|CDD|185658 PTZ00480, PTZ00480, serine/threonine-protein phosphatase;
Provisional.
Length = 320
Score = 25.4 bits (55), Expect = 9.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 7 LVLICAAHQLVRADYDVFNR 26
L LIC AHQ+V Y+ F++
Sbjct: 243 LDLICRAHQVVEDGYEFFSK 262
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
0.323 0.140 0.463
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,973,455
Number of extensions: 498869
Number of successful extensions: 400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 27
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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 (21.9 bits)
S2: 53 (24.2 bits)