RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11113
(699 letters)
>gnl|CDD|220155 pfam09258, Glyco_transf_64, Glycosyl transferase family 64 domain.
Members of this family catalyze the transfer reaction of
N-acetylglucosamine and N-acetylgalactosamine from the
respective UDP-sugars to the non-reducing end of
[glucuronic acid]beta 1-3[galactose]beta
1-O-naphthalenemethanol, an acceptor substrate analog of
the natural common linker of various
glycosylaminoglycans. They are also required for the
biosynthesis of heparan-sulphate.
Length = 244
Score = 193 bits (493), Expect = 5e-57
Identities = 67/137 (48%), Positives = 89/137 (64%), Gaps = 2/137 (1%)
Query: 553 FTIIILT-YERDQVLINSLSRLNNLPYLNKVVVVWNSVQPPREDLRWPDIGVPVVVVRTN 611
FT +I T Y R +L L+ P+L K+VV+WN+ +PP E +WP VP+ V+RT
Sbjct: 1 FTAVINTYYSRIDLLRKLLNHYAGSPHLAKIVVLWNNPKPPPELSKWPSPAVPLTVIRTK 60
Query: 612 TNDLNNRFKPYDVIETEAVLNMDDDVYLRHDEIMFAFRVWREQRDRIVGFPGRYHAWDQN 671
N LNNRF PY IET+AVL++DDD+ L DE+ FAF VW+ DRIVGFP R H WD
Sbjct: 61 RNSLNNRFLPYPEIETDAVLSLDDDILLSTDELDFAFSVWQSFPDRIVGFPPRSHFWD-L 119
Query: 672 NQGGWLYNSNYSCELSM 688
++G W Y S ++ + SM
Sbjct: 120 SKGRWGYTSEWTNDYSM 136
>gnl|CDD|217320 pfam03016, Exostosin, Exostosin family. The EXT family is a family
of tumour suppressor genes. Mutations of EXT1 on 8q24.1,
EXT2 on 11p11-13, and EXT3 on 19p have been associated
with the autosomal dominant disorder known as hereditary
multiple exostoses (HME). This is the most common known
skeletal dysplasia. The chromosomal locations of other
EXT genes suggest association with other forms of
neoplasia. EXT1 and EXT2 have both been shown to encode
a heparan sulphate polymerase with both D-glucuronyl
(GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC)
transferase activities. The nature of the defect in
heparan sulphate biosynthesis in HME is unclear.
Length = 292
Score = 80.9 bits (200), Expect = 1e-16
Identities = 69/362 (19%), Positives = 114/362 (31%), Gaps = 127/362 (35%)
Query: 87 LTSGFPMFVYDPEKYY-----PAWKISLFLKST------IYQALKFNPHFTSNPKEACVF 135
G ++VYD + + + S +L +++++ + T +P EA +F
Sbjct: 1 SCKGLKVYVYDLPRRFNLLEDVLPETSWYLTHQYAAESILHKSILNSRCRTLDPDEADLF 60
Query: 136 VVLIGESDVLFSN-----------VQDLYKLPYWGNNVGTELF----------------- 167
V S + +N V+ L LPYW + G +
Sbjct: 61 FVPFYTSLSVGTNAVERDLLPSELVEWLESLPYWNRSGGRDHIIVNSHPFGGSAFDRLPA 120
Query: 168 ------------------RIRPKVDLVLPPGVGLPGGDIWNECPYLLPARRKYLLSYQGS 209
+ RP D+ LP D + P++RK LL + G
Sbjct: 121 LNNNTILAVLAGGGFSEDQFRPGFDVPLPAYFHPNSVDDLES-DGMPPSKRKTLLFFAG- 178
Query: 210 GRRIHTQTPGVEEERITKPNDGDRDNSPSIEASSLTKYLTTSTSDLFHFDWSCVSSSDVC 269
P + + L + S + SC + +
Sbjct: 179 -----------------GPRPAGKGALANAIRDLLIEECKNSPDFQCEGNQSCGNPEN-- 219
Query: 270 YSESVRSEVLHQSTFVLIYADDLSRWKLDNEDMNNGTDKRSDKTRNRHSDEETVEDDRAE 329
E+L S F L+ D
Sbjct: 220 -----YMELLRSSRFCLVPPGD-------------------------------------- 236
Query: 330 RYASTIGIQMRLYEALKYGAVPVIVGGDNVMLPFEEVLDWNKILIPLPVARIPELHLLLR 389
S RL++AL+ G +PVI+ D LPFE+V+DW+K + +P IP L +LR
Sbjct: 237 TPTS-----PRLFDALRAGCIPVIIS-DGWELPFEDVIDWSKFSVRVPENDIPSLPEILR 290
Query: 390 SI 391
+I
Sbjct: 291 AI 292
>gnl|CDD|224137 COG1216, COG1216, Predicted glycosyltransferases [General function
prediction only].
Length = 305
Score = 32.5 bits (74), Expect = 0.66
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 553 FTIIILTYERDQVLINSLSRLNNLPYLNKVVVV 585
+III+TY R + L+ L+ L Y + V+VV
Sbjct: 5 ISIIIVTYNRGEDLVECLASLAAQTYPDDVIVV 37
>gnl|CDD|222281 pfam13641, Glyco_tranf_2_3, Glycosyltransferase like family 2.
Members of this family of prokaryotic proteins include
putative glucosyltransferase, which are involved in
bacterial capsule biosynthesis.
Length = 229
Score = 32.3 bits (74), Expect = 0.71
Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 16/99 (16%)
Query: 552 QFTIIILTYERDQVLINSLSRLNNLPY--LNKVVVVWNSVQPPREDLR-----WPDIGVP 604
+ +++ T+ D+VL +L + Y L +VVV S + R +PD+ V
Sbjct: 2 RVAVVVPTWNEDKVLGRTLRSILAQDYPRLEVIVVVDGSDDETLDVARELAAAYPDVRVH 61
Query: 605 VVVVRTNTNDLNNRFKPY------DVIETEAVLNMDDDV 637
VV K I+++ V+ +D D
Sbjct: 62 VVR---RPRPPGPTGKARALNEALRAIKSDLVVLLDADS 97
>gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Ornithine and Diaminopimelate
Decarboxylases, and Related Enzymes. This family
includes eukaryotic ornithine decarboxylase (ODC, EC
4.1.1.17), diaminopimelate decarboxylase (DapDC, EC
4.1.1.20), plant and prokaryotic biosynthetic arginine
decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine
decarboxylase (CANSDC), and ODC-like enzymes from
diverse bacterial species. These proteins are fold type
III PLP-dependent enzymes that catalyze essential steps
in the biosynthesis of polyamine and lysine. ODC and
ADC participate in alternative pathways of the
biosynthesis of putrescine, which is the precursor of
aliphatic polyamines in many organisms. ODC catalyzes
the direct synthesis of putrescine from L-ornithine,
while ADC converts L-arginine to agmatine, which is
hydrolysed to putrescine by agmatinase in a pathway that
exists only in plants and bacteria. DapDC converts
meso-2,6-diaminoheptanedioate to L-lysine, which is the
final step of lysine biosynthesis. CANSDC catalyzes the
decarboxylation of carboxynorspermidine, which is the
last step in the synthesis of norspermidine. The
PLP-dependent decarboxylases in this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. Prokaryotic ornithine, lysine and
biodegradative arginine decarboxylases are fold type I
PLP-dependent enzymes and are not included in this
family.
Length = 368
Score = 31.5 bits (72), Expect = 1.7
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 92 PMFVYDPE---KYYPAWKISLFLKSTIYQALKFNPH 124
P +VYD + +Y A K +L ++ A+K NP+
Sbjct: 2 PFYVYDLDIIRAHYAALKEALPSGVKLFYAVKANPN 37
>gnl|CDD|217204 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase,
carbamoyl-P binding domain.
Length = 140
Score = 29.8 bits (68), Expect = 2.4
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 329 ERYASTIGI----QMRLYEALKYGAVPVIVGGDNVMLPFEEVLD 368
RY I I L E KY +VPVI GD+ P + + D
Sbjct: 90 SRYVDAIVIRHPSHGALEELAKYSSVPVINAGDDHEHPTQALAD 133
>gnl|CDD|132997 cd00761, Glyco_tranf_GTA_type, Glycosyltransferase family A (GT-A)
includes diverse families of glycosyl transferases with
a common GT-A type structural fold.
Glycosyltransferases (GTs) are enzymes that synthesize
oligosaccharides, polysaccharides, and glycoconjugates
by transferring the sugar moiety from an activated
nucleotide-sugar donor to an acceptor molecule, which
may be a growing oligosaccharide, a lipid, or a protein.
Based on the stereochemistry of the donor and acceptor
molecules, GTs are classified as either retaining or
inverting enzymes. To date, all GT structures adopt one
of two possible folds, termed GT-A fold and GT-B fold.
This hierarchy includes diverse families of glycosyl
transferases with a common GT-A type structural fold,
which has two tightly associated beta/alpha/beta domains
that tend to form a continuous central sheet of at least
eight beta-strands. The majority of the proteins in this
superfamily are Glycosyltransferase family 2 (GT-2)
proteins. But it also includes families GT-43, GT-6,
GT-8, GT13 and GT-7; which are evolutionarily related to
GT-2 and share structure similarities.
Length = 156
Score = 29.8 bits (67), Expect = 3.0
Identities = 26/120 (21%), Positives = 38/120 (31%), Gaps = 12/120 (10%)
Query: 555 IIILTYERDQVLINSLSRLNNLPYLN-KVVVV--WNSVQPPREDLRWPDIGVPVVVVRTN 611
+II Y + L L L Y N +V+VV ++ + V+ V
Sbjct: 1 VIIPAYNEEPYLERCLESLLAQTYPNFEVIVVDDGSTDGTLEILEEYAKKDPRVIRVINE 60
Query: 612 TND-----LNNRFKPYDVIETEAVLNMDDDVYLRHDEIMFAFRVWREQRDR-IVGFPGRY 665
N N K E +L +D D L D + + VG PG
Sbjct: 61 ENQGLAAARNAGLK---AARGEYILFLDADDLLLPDWLERLVAELLADPEADAVGGPGNL 117
>gnl|CDD|132565 TIGR03526, selenium_YgeY, putative selenium metabolism hydrolase.
SelD, selenophosphate synthase, is the selenium donor
protein for both selenocysteine and selenouridine
biosynthesis systems, but it occurs also in a few
prokaryotes that have neither of those pathways. The
method of partial phylogenetic profiling , starting from
such orphan-selD genomes, identifies this protein as one
of those most strongly correlated to SelD occurrence.
Its distribution is also well correlated with that of
family TIGR03309, a putative accessory protein of labile
selenium (non-selenocysteine) enzyme maturation. This
family includes the uncharacterized YgeY of Escherichia
coli, and belongs to a larger family of metalloenzymes
in which some are known peptidases, others enzymes of
different types.
Length = 395
Score = 30.2 bits (68), Expect = 3.6
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 78 ECFDFSRCSLTSGFPMFVYDPEKYYPAWKI 107
E +++ R S T VY E Y+P W +
Sbjct: 287 EMYEYDRPSYTG----LVYPTECYFPTWVL 312
>gnl|CDD|204102 pfam08942, DUF1919, Domain of unknown function (DUF1919). This
domain has no known function. It is found in various
hypothetical and putative bacterial proteins.
Length = 198
Score = 29.6 bits (67), Expect = 4.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 555 IIILTYERDQVLINSLSRLNNLPYLNKVV 583
+ + +RD L +NLPY NKV+
Sbjct: 121 LFVKFTDRDGCTEELLKEFDNLPYKNKVI 149
>gnl|CDD|193526 cd05649, M20_ArgE_DapE_like4, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. This group includes the
hypothetical protein ygeY from Escherichia coli, a
putative deacetylase, but many in this subfamily are
classified as unassigned peptidases. ArgE/DapE enzymes
catalyze analogous reactions and share a common
activator, the metal ion (usually Co2+ or Zn2+). ArgE
catalyzes a broad range of substrates, including
N-acetylornithine, alpha-N-acetylmethionine and
alpha-N-formylmethionine, while DapE catalyzes the
hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP)
to L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly bacterial and archaeal, and have
been inferred by homology as being related to both ArgE
and DapE.
Length = 376
Score = 29.9 bits (68), Expect = 4.7
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 94 FVYDPEKYYPAWKI---SLFLKSTI--YQALKFNP 123
V + E+Y+PAW +K+ + Y+AL +P
Sbjct: 283 EVIEAERYFPAWLNEEDHELVKAALEAYKALFGDP 317
>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA;
Provisional.
Length = 921
Score = 30.0 bits (68), Expect = 5.3
Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 20/56 (35%)
Query: 375 PLPVARIPELHLLLRSISDEDIVAFRHQGR--QVFTRYLATLQSQMDTLVAVVRDR 428
LP R+ EL G + + + L TL Q DTL V +R
Sbjct: 343 RLPENRLDEL------------------GSIAKAYNQLLDTLNEQYDTLENKVAER 380
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 29.1 bits (66), Expect = 6.2
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 215 TQTPGVEEERITKP 228
T TPG EEE TKP
Sbjct: 187 TDTPGFEEENKTKP 200
>gnl|CDD|238897 cd01916, ACS_1, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
decarbonylase, is found in acetogenic and methanogenic
organisms and is responsible for the synthesis and
breakdown of acetyl-CoA. ACS forms a heterotetramer
with carbon monoxide dehydrogenase (CODH) consisting of
two ACS and two CODH subunits. CODH reduces carbon
dioxide to carbon monoxide and ACS then synthesizes
acetyl-CoA from carbon monoxide, CoA, and a methyl group
donated by another protein (CoFeSP). ACS has three
structural domains, an N-terminal rossman fold domain
with a helical region at its N-terminus which interacts
with CODH, and two alpha + beta fold domains. A Ni-Fe-S
center referred to as the A-cluster is located in the
C-terminal domain. A large cavity exists between the
three domains which may bind CoA.
Length = 731
Score = 29.7 bits (67), Expect = 6.3
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 341 LYEALKYGAVPVIVGGDNVMLPFEEVLDWN--KILIPLPVARIP 382
L EA K G PVI D +ML +V D + KI+ L +IP
Sbjct: 281 LEEAQKLGI-PVIATNDKIMLGLPDVTDEDPDKIVEDLVSGKIP 323
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 27.3 bits (61), Expect = 7.3
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 609 RTNTNDLNNRFKPYDVIETEAVLNMDDDVYLRHDEIMFAFRVWREQRD 656
T ++L RF+P+ IE + ++ R D + F +R D
Sbjct: 13 DTTRSELRQRFQPFGEIE-------EITLHFRDDGDNYGFVTYRYACD 53
>gnl|CDD|147379 pfam05165, GGDN, GGDN family. I have named this protein family of
unknown function GGDN after the most conserved motif.
The proteins are 200-270 amino acids in length.
Length = 246
Score = 28.7 bits (64), Expect = 8.5
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 343 EALKYGAVPVIVGGDNVMLPFEEV 366
K GA+ +GGDN M P +
Sbjct: 165 VLEKIGALTQFIGGDNFMAPCNGI 188
>gnl|CDD|184156 PRK13575, PRK13575, 3-dehydroquinate dehydratase; Provisional.
Length = 238
Score = 28.9 bits (65), Expect = 9.0
Identities = 9/39 (23%), Positives = 20/39 (51%)
Query: 13 DQIKQDILHYQDKLDKLKISINQAQLAHTESLRQNSPQL 51
+ + Q I H D +D +++ I+Q + + L + +L
Sbjct: 18 ETLIQKINHRIDAIDIIELRIDQWENVTVDQLAEMITKL 56
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 0.137 0.419
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,721,834
Number of extensions: 3679208
Number of successful extensions: 3180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3175
Number of HSP's successfully gapped: 26
Length of query: 699
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 595
Effective length of database: 6,324,786
Effective search space: 3763247670
Effective search space used: 3763247670
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 (21.7 bits)
S2: 62 (27.7 bits)