RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4654
(559 letters)
>gnl|CDD|149348 pfam08235, LNS2, LNS2 (Lipin/Ned1/Smp2). This domain is found in
Saccharomyces cerevisiae protein SMP2, proteins with an
N-terminal lipin domain (Pfam: PF04571) and
phosphatidylinositol transfer proteins. SMP2 (also known
as PAH1) is involved in plasmid maintenance and
respiration, and has been identified as a Mg2+-dependent
phosphatidate phosphatase (EC:3.1.3.4) that contains a
haloacid dehalogenase (HAD)-like domain. Lipin proteins
are involved in adipose tissue development and insulin
resistance.
Length = 156
Score = 154 bits (390), Expect = 2e-44
Identities = 62/157 (39%), Positives = 82/157 (52%), Gaps = 26/157 (16%)
Query: 380 VVFS-VDGSFTAS------VSVTGRDPKVRAGAVDIVRHWQELGYLIIYITGRPDMQQGR 432
VV S +DG+ TAS +S+ G+D V AG VD+VR QE GYLIIY+T RPD Q R
Sbjct: 1 VVISDIDGTITASDALGHILSIMGKD-WVHAGVVDLVRKIQENGYLIIYLTARPDGQADR 59
Query: 433 VLSWLSQH-----NFPHGLVSFA-DGLSPGF---------LGHKASYLKSLIQD--HGVV 475
++LSQH N PHG V + D L L K + L+ + Q +
Sbjct: 60 TRAYLSQHKQDGYNLPHGPVILSPDRLFAALHREVILKKPLVFKIACLRDIRQLFPNRNP 119
Query: 476 IHAAYGS-NKDVSVYTSVGLKPRSIYIVGKVSKKHQS 511
+A +G+ KDV VY SVG+ P I+ V + HQ
Sbjct: 120 FYAGFGNRIKDVIVYRSVGVPPSRIFTVNPKGEVHQE 156
>gnl|CDD|197870 smart00775, LNS2, This domain is found in Saccharomyces cerevisiae
protein SMP2, proteins with an N-terminal lipin domain
and phosphatidylinositol transfer proteins. SMP2 is
involved in plasmid maintenance and respiration. Lipin
proteins are involved in adipose tissue development and
insulin resistance.
Length = 157
Score = 153 bits (388), Expect = 4e-44
Identities = 46/158 (29%), Positives = 69/158 (43%), Gaps = 26/158 (16%)
Query: 379 VVVFSVDGSFTAS------VSVTGRDPKVRAGAVDIVRHWQELGYLIIYITGRPDMQQGR 432
+V+ +DG+ T S V + G+D G + R Q GY I+Y+T RP Q R
Sbjct: 1 IVISDIDGTITKSDVLGHVVPIIGKD-WTHPGVAKLYRDIQNNGYKILYLTARPIGQADR 59
Query: 433 VLSWLSQ-----HNFPHGLVSFA-DGLSPGF---------LGHKASYLKSLIQ---DHGV 474
S+LSQ HN PHG V + D L K + L+ + G
Sbjct: 60 TRSYLSQIKQDGHNLPHGPVLLSPDRLFAALHREVISKKPEVFKIACLRDIKNLFPPQGN 119
Query: 475 VIHAAYGSN-KDVSVYTSVGLKPRSIYIVGKVSKKHQS 511
+A +G+ DV Y++VG+ P I+ + + HQ
Sbjct: 120 PFYAGFGNRITDVISYSAVGIPPSRIFTINPKGEVHQE 157
>gnl|CDD|217255 pfam02862, DDHD, DDHD domain. The DDHD domain is 180 residues long
and contains four conserved residues that may form a
metal binding site. The domain is named after these four
residues. This pattern of conservation of metal binding
residues is often seen in phosphoesterase domains. This
domain is found in retinal degeneration B proteins, as
well as a family of probable phospholipases. It has been
shown that this domain is found in a longer C terminal
region that binds to PYK2 tyrosine kinase. These
proteins have been called N-terminal domain-interacting
receptor (Nir1, Nir2 and Nir3). This suggests that this
region is involved in functionally important
interactions in other members of this family.
Length = 219
Score = 126 bits (319), Expect = 2e-33
Identities = 50/199 (25%), Positives = 78/199 (39%), Gaps = 12/199 (6%)
Query: 43 SPSVASRQGDVIQRPPVQQVYNLFHPTDPIAVRLEPLISARFSLLAPVNIPRYQQFPLGK 102
S S + + P + +YN+FHPTDP+A RLEPL+ ++ L PV IP ++ LG
Sbjct: 30 SLSYVAGEDGTYGCPACKNLYNIFHPTDPVAYRLEPLVDPEYANLKPVLIPHAKKSKLGA 89
Query: 103 SQSTSVAQAL---LIRMVTQKWWGSKRIDYALYCPEGLANFPTNALPHLFHASFWESCDV 159
+ + + + V WG+ + + T+ S S
Sbjct: 90 LELLESLTNIGKAVKQSVGSTTWGAGNEIASGLRNSSASRSSTDE------KSADSSTIS 143
Query: 160 IAFILRQVNNLLTYFRAREIGKAPRKVTQKWWGSKRIDYALYCPEGLANFPTNALPHLFH 219
+ R + + G+ RIDY L EG+ H
Sbjct: 144 RLSPSNVELETSEFTREEKKSERAELRLGALNGNGRIDYVLQ--EGVLE-NQYLSALSSH 200
Query: 220 ASFWESCDVIAFILRQIGR 238
S+WES DV F+L++I R
Sbjct: 201 VSYWESEDVALFLLKEILR 219
>gnl|CDD|227415 COG5083, SMP2, Uncharacterized protein involved in plasmid
maintenance [General function prediction only].
Length = 580
Score = 55.3 bits (133), Expect = 6e-08
Identities = 52/239 (21%), Positives = 77/239 (32%), Gaps = 33/239 (13%)
Query: 321 SGEWVLMSTEVTDKTGRVSYTLPEDH--KLSYGMYPVKMVVRGDHTSVDFYLAVVPPRTE 378
W + VTD G + + L YG +K V G Y+ V +
Sbjct: 317 EPSWNKIGEAVTDYNGTIKLNSDQLRNLNLKYGKNLLKFYVEGGKAIATMYIFVWRNNKK 376
Query: 379 VVVFSVDGSFTAS------VSVTGRD---PKVRAGAVDIVRHWQELGYLIIYITGRPDMQ 429
+VV +DG+ T S + G+D V DI R+ GY I Y+T R Q
Sbjct: 377 IVVSDIDGTITKSDALGHVKQMIGKDWTHNGVAKLYTDIDRN----GYKIKYLTSRSYGQ 432
Query: 430 ---QGRVL-------SWLSQHNFPHGLVSFADGLSPGFLGH-----KASYLKSLIQDHG- 473
L L L + K +YL L
Sbjct: 433 ADSTRSYLRNIEQNGYKLPDGPVILSPDRTMAALYRELILRKPEVFKIAYLNDLKSLFIE 492
Query: 474 -VVIHAAYGSNK-DVSVYTSVGLKPRSIYIVGKVSKKHQSQATVLSDGYAAHLTALQQH 530
+A +G+ DV Y++VG+ I+ + K + H V + L H
Sbjct: 493 FDPFYAGFGNRITDVISYSNVGIPKSRIFTINKNGEVHGELLIVSYRSSYKQMNELVDH 551
>gnl|CDD|233532 TIGR01689, EcbF-BcbF, capsule biosynthesis phosphatase. This model
describes a small family of highly conserved proteins
(>60% ID). Two of these, BcbF and EcbF of Pasteurella
multocida are believed to be part of the capsule
polysaccharide biosynthesis machinery because they are
cotranscribed from a locus devoted to that purpose. In
pasteurella there are six different variant capsules
(A-F), and these proteins are found only in B and E. The
other two species in which this gene is (currently)
found are both also pathogenic. These proteins are also
members of the IIIC (TIGR01681) subfamily of the
Haloacid Dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. All of the
characterized enzymes within subfamily III are
phosphatases, and all of the active site residues
characteristic of HAD-superfamily phosphatases are
present in this subfamily. Due to the likelihood that
the substrates of these enzymes are different depending
on the nature of the particular polysaccharides
associated with each species, this model has been
classified as a subfamily despite the close homology.
Length = 126
Score = 31.0 bits (70), Expect = 0.54
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 14/78 (17%)
Query: 380 VVFSVDGSFTASVSVTGRDPKVRAGAVDIVRHWQELGYLIIYITGRPDMQ--QGRV---- 433
+V +D + T + + + ++ +RH++ LG+ I+ + R +M+ +G V
Sbjct: 4 LVMDLDNTITLTENGDYANVAPILAVIEKLRHYKALGFEIVISSSR-NMRTYEGNVGKIN 62
Query: 434 -------LSWLSQHNFPH 444
+ WL+QHN P+
Sbjct: 63 IHTLPIIILWLNQHNVPY 80
>gnl|CDD|100114 cd05822, TLP_HIUase, HIUase (5-hydroxyisourate hydrolase) catalyzes
the second step in a three-step ureide pathway in which
5-hydroxyisourate (HIU), a product of the uricase (urate
oxidase) reaction, is hydrolyzed to
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU).
HIUase has high sequence similarity with transthyretins
and is a member of the transthyretin-like protein (TLP)
family. HIUase is distinguished from transthyretins by
a conserved signature motif at its C-terminus that forms
part of the active site. In HIUase, this motif is YRGS,
while transthyretins have a conserved TAVV sequence in
the same location. Most HIUases are cytosolic but in
plants and slime molds, they are peroxisomal based on
the presence of N-terminal periplasmic localization
sequences. HIUase forms a homotetramer with each
subunit consisting of eight beta-strands arranged in two
sheets and a short alpha-helix. The central channel of
the tetramer contains two independent binding sites,
each located between a pair of subunits.
Length = 112
Score = 30.6 bits (70), Expect = 0.57
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 311 VDVHLIKEPPSGEWVLMSTEVTDKTGRVSYTLPEDHKLSYGMY 353
V V L + +G W L++T VT+ GR LP +L+ G Y
Sbjct: 19 VAVTLYRLDGNG-WTLLATGVTNADGRCDDLLPPGAQLAAGTY 60
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 31.8 bits (73), Expect = 1.0
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 379 VVVFSVDGSFTASVSVTGRDPKVRAGAVDIVRHWQELGYLIIYITG 424
VV +VDG +++ D +R A + + + LG ++ +TG
Sbjct: 519 VVFVAVDGKLVGVIAL--ADE-LRPDAKEAIAALKALGIKVVMLTG 561
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 31.1 bits (71), Expect = 1.3
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 12/73 (16%)
Query: 380 VVFSVDGSFTASVSVTGRDP---------KVRAGAVDIVRHWQELGYLIIYITGRPDMQQ 430
V+F +DG+ + GR P K V++V+ ++ GY II ++GR + +
Sbjct: 161 VIFDIDGTLA---KMGGRSPYDWTKVKEDKPNPMVVELVKMYKAAGYEIIVVSGRDGVCE 217
Query: 431 GRVLSWLSQHNFP 443
+ WL Q +
Sbjct: 218 EDTVEWLRQTDIW 230
>gnl|CDD|217719 pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid
phosphatase). This family proteins includes acid
phosphatases and a number of vegetative storage
proteins.
Length = 213
Score = 30.8 bits (70), Expect = 1.4
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 394 VTGRDPKVRAGAVDIVRHWQELGYLIIYITGRPD 427
V + GA+++ + ELG I +++GR +
Sbjct: 97 VNKGEAPALPGALELYNYLVELGVKIFFVSGRSE 130
>gnl|CDD|201317 pfam00576, Transthyretin, HIUase/Transthyretin family. This family
includes transthyretin that is a thyroid hormone-binding
protein that transports thyroxine from the bloodstream
to the brain. However, most of the sequences listed in
this family do not bind thyroid hormones. They are
actually enzymes of the purine catabolism that catalyze
the conversion of 5-hydroxyisourate (HIU) to OHCU. HIU
hydrolysis is the original function of the family and is
conserved from bacteria to mammals; transthyretins arose
by gene duplications in the vertebrate lineage. HIUases
are distinguished in the alignment from the conserved
C-terminal YRGS sequence.
Length = 111
Score = 29.5 bits (67), Expect = 1.5
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 311 VDVHLIKEPPSGEWVLMSTEVTDKTGRVSYTLPEDH 346
V V L + G W L++T T+ GRV L +
Sbjct: 19 VAVKLFRLTEGGGWELLATGKTNADGRVHPLLTGET 54
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 30.0 bits (68), Expect = 1.5
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 379 VVVFSVDGSFT--ASVSVTGRDPKVRAGAVDIVRHWQELGYLIIYITGRP 426
V+F +DG+ + ++ G + ++ +E G + T +
Sbjct: 1 AVLFDLDGTLLDSEPGIAEIEELELYPGVKEALKELKEKGIKLALATNKS 50
>gnl|CDD|200221 TIGR02962, hdxy_isourate, hydroxyisourate hydrolase. Members of
this family, hydroxyisourate hydrolase, represent a
distinct clade of transthyretin-related proteins.
Bacterial members typically are encoded next to
ureidoglycolate hydrolase and often near either xanthine
dehydrogenase or xanthine/uracil permease genes and have
been demonstrated to have hydroxyisourate hydrolase
activity. In eukaryotes, a clade separate from the
transthyretins (a family of thyroid-hormone binding
proteins) has also been shown to have HIU hydrolase
activity in urate catabolizing organisms. Transthyretin,
then, would appear to be the recently diverged paralog
of the more ancient HIUH family [Purines, pyrimidines,
nucleosides, and nucleotides, Other].
Length = 112
Score = 29.4 bits (67), Expect = 1.7
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 311 VDVHLIKEPPSGEWVLMSTEVTDKTGRVSYTLPEDHKLSYGMY 353
V V L + SG W ++ VT+ GR LPE L+ G+Y
Sbjct: 19 VPVTLYRLDGSG-WTPLAEGVTNADGRCDGPLPEGETLAAGIY 60
>gnl|CDD|128547 smart00251, SAM_PNT, SAM / Pointed domain. A subfamily of the SAM
domain.
Length = 82
Score = 28.0 bits (63), Expect = 3.6
Identities = 6/36 (16%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 219 HASFWESCDVIAFILRQIGRFDMAPAMGTDDKDLEG 254
W V+ ++ + F ++P + D+ G
Sbjct: 16 DPQLWTEDHVLEWLEWAVKEFSLSP-IDFSKFDMSG 50
>gnl|CDD|176040 cd08394, C2A_Munc13, C2 domain first repeat in Munc13 (mammalian
uncoordinated) proteins. C2-like domains are thought to
be involved in phospholipid binding in a Ca2+
independent manner in both Unc13 and Munc13.
Caenorabditis elegans Unc13 has a central domain with
sequence similarity to PKC, which includes C1 and
C2-related domains. Unc13 binds phorbol esters and DAG
with high affinity in a phospholipid manner. Mutations
in Unc13 results in abnormal neuronal connections and
impairment in cholinergic neurotransmission in the
nematode. Munc13 is the mammalian homolog which are
expressed in the brain. There are 3 isoforms (Munc13-1,
-2, -3) and are thought to play a role in
neurotransmitter release and are hypothesized to be
high-affinity receptors for phorbol esters. Unc13 and
Munc13 contain both C1 and C2 domains. There are two C2
related domains present, one central and one at the
carboxyl end. Munc13-1 contains a third C2-like domain.
Munc13 interacts with syntaxin, synaptobrevin, and
synaptotagmin suggesting a role for these as scaffolding
proteins. C2 domains fold into an 8-standed
beta-sandwich that can adopt 2 structural arrangements:
Type I and Type II, distinguished by a circular
permutation involving their N- and C-terminal beta
strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-II topology.
Length = 127
Score = 28.6 bits (64), Expect = 3.6
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 311 VDVHLIKEPPSGEWVLMSTEVTDKTGRVSYTL-PEDHKL 348
+ E GEW+ + +EV K G++ T P H++
Sbjct: 83 STIRQSNEEGPGEWLTLDSEVNMKNGQIVGTKDPTFHRI 121
>gnl|CDD|107291 cd06296, PBP1_CatR_like, Ligand-binding domain of a LacI-like
transcriptional regulator, CatR which is involved in
catechol degradation. This group includes the
ligand-binding domain of a LacI-like transcriptional
regulator, CatR which is involved in catechol
degradation. This group belongs to the the LacI-GalR
family repressors that are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the sugar-binding domain of ABC-type
transport systems that contain the type I periplasmic
binding protein-like fold. As also observed in the
periplasmic binding proteins, the C-terminal domain of
the bacterial transcription repressor undergoes a
conformational change upon ligand binding which in turn
changes the DNA binding affinity of the repressor.
Length = 270
Score = 29.5 bits (67), Expect = 4.3
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 403 AGAVDIVRHWQELGYL-IIYITGRPDMQQGR 432
AG + H ELG+ I +ITG PD+ R
Sbjct: 103 AGGLAATEHLLELGHRRIGFITGPPDLLCSR 133
>gnl|CDD|100039 cd00710, LbH_gamma_CA, Gamma carbonic anhydrases (CA): Carbonic
anhydrases are zinc-containing enzymes that catalyze the
reversible hydration of carbon dioxide in a two-step
mechanism, involving the nucleophilic attack of a
zinc-bound hydroxide ion on carbon dioxide, followed by
the regeneration of the active site by ionization of the
zinc-bound water molecule and removal of a proton from
the active site. They are ubiquitous enzymes involved in
fundamental processes like photosynthesis, respiration,
pH homeostasis and ion transport. There are three
distinct groups of carbonic anhydrases - alpha, beta
and gamma - which show no significant sequence identity
or structural similarity. Gamma CAs are homotrimeric
enzymes, with each subunit containing a left-handed
parallel beta helix (LbH) structural domain.
Length = 167
Score = 28.4 bits (64), Expect = 6.0
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 16/47 (34%)
Query: 466 KSLIQDHGVVIHAAYGSNKDVSVYTSVGLKPRSIYIVGKVSKKHQSQ 512
IQD GVVIH L+ S++I VS H +
Sbjct: 48 NVNIQD-GVVIH---------------ALEGYSVWIGKNVSIAHGAI 78
>gnl|CDD|232918 TIGR00321, dhys, deoxyhypusine synthase. Deoxyhypusine synthase is
responsible for the first step in creating hypusine.
Hypusine is a modified amino acid found in eukaryotes
and in archaea in their respective forms of initiation
factor 5A. Its presence is confirmed in archaeal genera
Pyrococcus (PMID:12761201), Sulfolobus, Halobacterium,
and Haloferax (PMID:10648545), but in an older report
was not detected in Methanococcus voltae (J Biol Chem
1987 Dec 5;262(34):16585-9). This family of apparent
orthologs has an unusual UPGMA difference tree, in which
the members from the archaea M. jannaschii and P.
horikoshii cluster with the known eukaryotic
deoxyhypusine synthases. Separated by a fairly deep
branch, although still strongly related, is a small
cluster of proteins from Methanobacterium
thermoautotrophicum and Archeoglobus fulgidus, the
latter of which has two [Protein fate, Protein
modification and repair].
Length = 301
Score = 28.5 bits (64), Expect = 8.5
Identities = 20/117 (17%), Positives = 39/117 (33%), Gaps = 16/117 (13%)
Query: 422 ITGRPDMQQGRVLSWLSQHNFPHGLVSFADGLSPGFLGHKASYLKSLIQDHGVVIHAAYG 481
I R + ++ + + P F L+ +G + + + + I
Sbjct: 155 IGKRINDKRSSIRYAAYKRKIP----IFCPALTDSSIGLMLFFYT---KKNSLRIDIV-- 205
Query: 482 SNKDVSVYTSVGLKPRS---IYIVGKVSKKHQSQATVLSDG--YAAHLTALQQHGGS 533
+D+ + I + G + K A +L +G YA +T Q GS
Sbjct: 206 --RDIRKLNDIVFNSERTGVIILGGGLPKHFILNACLLREGADYAVQITTDQPQDGS 260
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.8 bits (65), Expect = 8.7
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 355 VKMVVRGDHTSVDF 368
KMV+ GD T +D
Sbjct: 271 SKMVITGDITQIDL 284
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
0.321 0.136 0.419
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,038,865
Number of extensions: 2855052
Number of successful extensions: 2258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2247
Number of HSP's successfully gapped: 26
Length of query: 559
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 457
Effective length of database: 6,413,494
Effective search space: 2930966758
Effective search space used: 2930966758
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: 62 (27.6 bits)