RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18038
(146 letters)
>gnl|CDD|238363 cd00707, Pancreat_lipase_like, Pancreatic lipase-like enzymes.
Lipases are esterases that can hydrolyze long-chain
acyl-triglycerides into di- and monoglycerides,
glycerol, and free fatty acids at a water/lipid
interface. A typical feature of lipases is "interfacial
activation," the process of becoming active at the
lipid/water interface, although several examples of
lipases have been identified that do not undergo
interfacial activation . The active site of a lipase
contains a catalytic triad consisting of Ser - His -
Asp/Glu, but unlike most serine proteases, the active
site is buried inside the structure. A "lid" or "flap"
covers the active site, making it inaccessible to
solvent and substrates. The lid opens during the process
of interfacial activation, allowing the lipid substrate
access to the active site.
Length = 275
Score = 121 bits (305), Expect = 1e-34
Identities = 46/84 (54%), Positives = 50/84 (59%), Gaps = 10/84 (11%)
Query: 55 GLDPAGPLFESQDPRSRLDSSDAQFVDVIHSNGENLILGGLGSWQPLGHVDFYPNGGRMQ 114
GLDPAGPLF DP RLD SDAQFVDVIH++G G LG QP+GH DFYPNGGR Q
Sbjct: 142 GLDPAGPLFSGADPEDRLDPSDAQFVDVIHTDG-----GLLGFSQPIGHADFYPNGGRDQ 196
Query: 115 KGCTNLFVGAVSDILWFQFSDHLR 138
GC + F H R
Sbjct: 197 PGCPKDIL-----SSDFVACSHQR 215
>gnl|CDD|215752 pfam00151, Lipase, Lipase.
Length = 329
Score = 94.4 bits (235), Expect = 4e-24
Identities = 38/84 (45%), Positives = 49/84 (58%), Gaps = 4/84 (4%)
Query: 55 GLDPAGPLFESQDPRSRLDSSDAQFVDVIHSNGENLILGGLGSWQPLGHVDFYPNGGRMQ 114
GLDPAGP F+ +RLD DA FVD IH++ + G+G+ Q +GHVDF+PNGG Q
Sbjct: 180 GLDPAGPYFKGTPELTRLDPGDADFVDAIHTDTRPIPGLGMGTSQRVGHVDFFPNGGSEQ 239
Query: 115 KGCTNLFVGAVSDILWFQFSDHLR 138
GC N V + F H+R
Sbjct: 240 PGCQNN----VLEGTQFVACAHMR 259
>gnl|CDD|132274 TIGR03230, lipo_lipase, lipoprotein lipase. Members of this
protein family are lipoprotein lipase (EC 3.1.1.34), a
eukaryotic triacylglycerol lipase active in plasma and
similar to pancreatic and hepatic triacylglycerol
lipases (EC 3.1.1.3). It is also called clearing factor.
It cleaves chylomicron and VLDL triacylglycerols; it
also has phospholipase A-1 activity.
Length = 442
Score = 79.6 bits (196), Expect = 3e-18
Identities = 33/63 (52%), Positives = 39/63 (61%)
Query: 55 GLDPAGPLFESQDPRSRLDSSDAQFVDVIHSNGENLILGGLGSWQPLGHVDFYPNGGRMQ 114
GLDPAGP FE D S L DA FVDV+H+N +G +P+GH+D YPNGG Q
Sbjct: 149 GLDPAGPTFEYADAPSTLSPDDADFVDVLHTNTRGSPDRSIGIQRPVGHIDIYPNGGTFQ 208
Query: 115 KGC 117
GC
Sbjct: 209 PGC 211
>gnl|CDD|238382 cd00741, Lipase, Lipase. Lipases are esterases that can hydrolyze
long-chain acyl-triglycerides into di- and
monoglycerides, glycerol, and free fatty acids at a
water/lipid interface. A typical feature of lipases is
"interfacial activation", the process of becoming active
at the lipid/water interface, although several examples
of lipases have been identified that do not undergo
interfacial activation . The active site of a lipase
contains a catalytic triad consisting of Ser - His -
Asp/Glu, but unlike most serine proteases, the active
site is buried inside the structure. A "lid" or "flap"
covers the active site, making it inaccessible to
solvent and substrates. The lid opens during the process
of interfacial activation, allowing the lipid substrate
access to the active site.
Length = 153
Score = 56.4 bits (136), Expect = 6e-11
Identities = 29/91 (31%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 55 GLDPAGPLFESQDPRSRLDSSDAQFVDVIHSNGENL-ILGGLGSWQPLGHVDFYPNGGRM 113
P + RLD SDA FVD I ++ + + L G P G +FY NGG+
Sbjct: 62 TFGPPRVGNAAFAED-RLDPSDALFVDRIVNDNDIVPRLPPGGEGYPHGGAEFYINGGKS 120
Query: 114 QKGCTNLFVGAVSD------ILWFQFSDHLR 138
Q GC + AV + DHLR
Sbjct: 121 QPGCCKNVLEAVDIDFGNIGLSGNGLCDHLR 151
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 28.8 bits (65), Expect = 1.0
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 5 KSLVEQASSIFRLYVQSG--RGFS-RVVL---IYSAC 35
+S+ E A+ I+R V G RG S V IY+AC
Sbjct: 115 ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAAC 151
>gnl|CDD|237846 PRK14876, PRK14876, conjugal transfer mating pair stabilization
protein TraN; Provisional.
Length = 928
Score = 28.3 bits (63), Expect = 1.5
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 10/51 (19%)
Query: 80 VDVIHSNGENLILGGLGSWQPLGHVDFYPNGGRMQKGCTNLFVGAVSDILW 130
+V+H ++ H N +GCT L+VG V D W
Sbjct: 222 CEVVHDYDAGVV----------KHYSGPYNLQSCGEGCTELWVGTVGDNYW 262
>gnl|CDD|233794 TIGR02239, recomb_RAD51, DNA repair protein RAD51. This eukaryotic
sequence family consists of RAD51, a protein involved in
DNA homologous recombination and repair. It is similar
in sequence the exclusively meiotic recombinase DMC1
(TIGR02238), to archaeal families RadA (TIGR02236) and
RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Length = 316
Score = 27.4 bits (61), Expect = 3.1
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 12 SSIFRLYVQSGRGFSRVVLIY-SAC 35
+S RL ++ GRG R+ IY S C
Sbjct: 272 ASTTRLSLRKGRGEQRICKIYDSPC 296
>gnl|CDD|176249 cd08289, MDR_yhfp_like, Yhfp putative quinone oxidoreductases.
yhfp putative quinone oxidoreductases (QOR). QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent
single electron transfer. QOR is a member of the medium
chain dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG
motif after the first mononucleotide contact half
allows the close contact of the coenzyme with the ADH
backbone. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. In human
ADH catalysis, the zinc ion helps coordinate the
alcohol, followed by deprotonation of a histidine, the
ribose of NAD, a serine, then the alcohol, which allows
the transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 326
Score = 27.3 bits (61), Expect = 3.2
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 52 MFPGLDPAGPLFESQDPR 69
PG+D AG + ES DPR
Sbjct: 59 FIPGIDLAGTVVESNDPR 76
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member
of the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin
cytoskeleton and secretory apparatus at the bud site.
It is believed that cdc42 interacts directly with RSR1
in vivo. In filamentous fungi, polar growth occurs at
the tips of hypha and at novel growth sites along the
extending hypha. In Ashbya gossypii, RSR1 is a key
regulator of hyphal growth, localizing at the tip
region and regulating in apical polarization of the
actin cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins.
Length = 168
Score = 27.1 bits (60), Expect = 3.4
Identities = 12/29 (41%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 8 VEQASSIFRLYVQSGRGFSRVVLIYSACS 36
EQ +++ LY++SG+GF +L+YS S
Sbjct: 59 TEQFTAMRELYIKSGQGF---LLVYSVTS 84
>gnl|CDD|177920 PLN02281, PLN02281, chlorophyllide a oxygenase.
Length = 536
Score = 27.4 bits (60), Expect = 3.4
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 61 PLFESQDPRSRLDSSDAQFVDV 82
PLF+ +DPRS+ +F+DV
Sbjct: 56 PLFDVEDPRSKAPPYKGKFLDV 77
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates
with a poor prognosis, suggesting a role for Rap2 in
breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c,
Rap1a, or Rap1b, is expressed in human red blood cells,
where it is believed to be involved in vesiculation. A
number of additional effector proteins for Rap2 have
been identified, including the RalGEFs RalGDS, RGL, and
Rlf, which also interact with Rap1 and Ras. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 26.7 bits (59), Expect = 4.1
Identities = 11/44 (25%), Positives = 27/44 (61%), Gaps = 9/44 (20%)
Query: 9 EQASSIFRLYVQSGRGFSRVVLIYSACSSFLILSNTFYSNLRTM 52
EQ +S+ LY+++G+GF +++YS +++ + +++ M
Sbjct: 60 EQFASMRDLYIKNGQGF---IVVYS------LVNQQTFQDIKPM 94
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or
Krev1 in the older literature. Rap1 proteins are
believed to perform different cellular functions,
depending on the isoform, its subcellular localization,
and the effector proteins it binds. For example, in rat
salivary gland, neutrophils, and platelets, Rap1
localizes to secretory granules and is believed to
regulate exocytosis or the formation of secretory
granules. Rap1 has also been shown to localize in the
Golgi of rat fibroblasts, zymogen granules, plasma
membrane, and the microsomal membrane of pancreatic
acini, as well as in the endocytic compartment of
skeletal muscle cells and fibroblasts. High expression
of Rap1 has been observed in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines; interestingly, in the SCCs, the active GTP-bound
form localized to the nucleus, while the inactive
GDP-bound form localized to the cytoplasm. Rap1 plays a
role in phagocytosis by controlling the binding of
adhesion receptors (typically integrins) to their
ligands. In yeast, Rap1 has been implicated in multiple
functions, including activation and silencing of
transcription and maintenance of telomeres. Rap1a,
which is stimulated by T-cell receptor (TCR)
activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 26.3 bits (58), Expect = 4.8
Identities = 13/41 (31%), Positives = 26/41 (63%), Gaps = 9/41 (21%)
Query: 9 EQASSIFRLYVQSGRGFSRVVLIYSACSSFLILSNTFYSNL 49
EQ +++ LY+++G+GF VL+YS I + + +++L
Sbjct: 60 EQFTAMRDLYMKNGQGF---VLVYS------ITAQSTFNDL 91
>gnl|CDD|234716 PRK00292, glk, glucokinase; Provisional.
Length = 316
Score = 26.7 bits (60), Expect = 5.2
Identities = 9/18 (50%), Positives = 9/18 (50%), Gaps = 4/18 (22%)
Query: 96 GSWQPL----GHVDFYPN 109
G W L GHVDF P
Sbjct: 149 GRWIVLPGEGGHVDFAPR 166
>gnl|CDD|177958 PLN02324, PLN02324, triacylglycerol lipase.
Length = 415
Score = 26.5 bits (58), Expect = 5.6
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 51 TMFPGLDPAG---------PLFESQDPRSRLDSSDAQ 78
++FP DP ++ + D RS D++ AQ
Sbjct: 160 SVFPVTDPKDNPRIGSGWLDIYTASDSRSPYDTTSAQ 196
>gnl|CDD|220591 pfam10131, PTPS_related, 6-pyruvoyl-tetrahydropterin synthase
related domain; membrane protein. This domain is found
in various bacterial hypothetical membrane proteins, as
well as in tetratricopeptide TPR_2 repeat protein. The
exact function of the domain has not, as yet, been
established.
Length = 620
Score = 26.6 bits (59), Expect = 5.8
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 121 FVGAVSDILWFQFSDHLRNLGW 142
+ ++ +LW F ++LR
Sbjct: 52 LIAVIAGLLWLLFPENLRVAFS 73
>gnl|CDD|99739 cd00615, Orn_deC_like, Ornithine decarboxylase family. This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD corresponds to ornithine
decarboxylase (ODC), arginine decarboxylase (ADC) and
lysine decarboxylase (LDC). ODC is a dodecamer composed
of six homodimers and catalyzes the decarboxylation of
tryptophan. ADC catalyzes the decarboxylation of
arginine and LDC catalyzes the decarboxylation of
lysine. Members of this family are widely found in all
three forms of life.
Length = 294
Score = 26.4 bits (59), Expect = 6.3
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 12/76 (15%)
Query: 20 QSGRGFSRVVLIYSACSSFLILSNTFYSNLRTMFPGLD----PAGPLFESQDPRSRLDSS 75
+ GRGF + + N F +++ T GLD P GP+ E+Q+ +R +
Sbjct: 23 KGGRGFRKSFYEF-------YGENLFKADV-TELTGLDDLLDPTGPIKEAQELAARAFGA 74
Query: 76 DAQFVDVIHSNGENLI 91
F V ++ N
Sbjct: 75 KHTFFLVNGTSSSNKA 90
>gnl|CDD|234216 TIGR03454, partition_RepB, plasmid partitioning protein RepB.
Members of this family are the RepB protein involved in
replicon partitioning. RepB is found, in general, as
part of a repABC operon in plasmids and small
chromosomes, separate from the main chromosome, in
various bacteria. This model describes a rather narrow
clade of proteins; it should be noted that additional
homologs scoring below the trusted cutoff have very
similar functions, although they may be named
differently [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 325
Score = 26.5 bits (59), Expect = 6.5
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 56 LDPAGPLFESQDPRSRLDSSDAQF---VDVIHSNGEN 89
LDPA L + R RLDS D F V+ I +G+
Sbjct: 67 LDPA--LIDPSFVRDRLDSDDEDFADLVESIREHGQQ 101
>gnl|CDD|117002 pfam08423, Rad51, Rad51. Rad51 is a DNA repair and recombination
protein and is a homologue of the bacterial ATPase RecA
protein.
Length = 261
Score = 26.1 bits (58), Expect = 6.7
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 12 SSIFRLYVQSGRGFSRVVLIYSA 34
+S RLY++ GRG RV IY +
Sbjct: 218 ASTTRLYLRKGRGEQRVCKIYDS 240
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 26.1 bits (58), Expect = 7.9
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 10 QASSIFRLYVQSGRGFSRVVLIY 32
AS+ RL ++ GRG R+ IY
Sbjct: 292 HASTT-RLSLRKGRGEQRICKIY 313
>gnl|CDD|182589 PRK10614, PRK10614, multidrug efflux system subunit MdtC;
Provisional.
Length = 1025
Score = 26.2 bits (58), Expect = 9.0
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 67 DPRSRLDSSDAQFVDVIHSNGENLILGGLGSWQP 100
DPR D S + + VI++ G+ + L WQP
Sbjct: 753 DPRYTQDISALEKMFVINNEGKAIPLSYFAKWQP 786
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
0.322 0.139 0.428
Gapped
Lambda K H
0.267 0.0817 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,303,446
Number of extensions: 636508
Number of successful extensions: 545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 542
Number of HSP's successfully gapped: 28
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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: 54 (24.4 bits)