RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14393
(114 letters)
>gnl|CDD|193524 cd05646, M20_AcylaseI_like, M20 Aminoacylase-I like subfamily.
Peptidase M20 family, Aminoacylase-I like (AcyI-like;
Acylase I; N-acyl-L-amino-acid amidohydrolase; EC
3.5.1.14) subfamily. Acylase I is involved in the
hydrolysis of N-acylated or N-acetylated amino acids
(except L-aspartate) and is considered as a potential
target of antimicrobial agents. Porcine AcyI is also
shown to deacetylate certain quorum-sensing
N-acylhomoserine lactones, while the rat enzyme has been
implicated in degradation of chemotactic peptides of
commensal bacteria. Prokaryotic arginine synthesis
usually involves the transfer of an acetyl group to
glutamate by ornithine acetyltransferase in order to
form ornithine. However, Escherichia coli
acetylornithine deacetylase (acetylornithinase, ArgE)
(EC 3.5.1.16) catalyzes the deacylation of
N2-acetyl-L-ornithine to yield ornithine and acetate.
Phylogenetic evidence suggests that the clustering of
the arg genes in one continuous sequence pattern arose
in an ancestor common to Enterobacteriaceae and
Vibrionaceae, where ornithine acetyltransferase was lost
and replaced by a deacylase.
Length = 391
Score = 184 bits (470), Expect = 1e-58
Identities = 65/112 (58%), Positives = 83/112 (74%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEEIGG GM FV T+ FKK+NVG ALDEG+ASPTE + +F GER+ W + I GTPG
Sbjct: 138 DEEIGGHDGMEKFVKTEEFKKLNVGFALDEGLASPTEEYRVFYGERSPWWVVITASGTPG 197
Query: 63 HGSLLHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINITMLS 114
HGS L +NTA EK+ ++ KF+ REE+ +LK+N LTIGDVT++N+TML
Sbjct: 198 HGSKLLDNTAGEKLMKVIEKFMEFREEQFQRLKSNGKLTIGDVTSVNLTMLK 249
>gnl|CDD|233615 TIGR01880, Ac-peptdase-euk, N-acyl-L-amino-acid amidohydrolase.
This model represents a family of eukaryotic
N-acyl-L-amino-acid amidohydrolases active on fatty acid
and acetyl amides of L-amino acids.
Length = 400
Score = 152 bits (385), Expect = 6e-46
Identities = 55/111 (49%), Positives = 72/111 (64%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEEIGG GM F TD FK +N+G ALDEG+ASP +V+ +F ER W + + PG PG
Sbjct: 145 DEEIGGHDGMEKFAKTDEFKALNLGFALDEGLASPDDVYRVFYAERVPWWVVVTAPGNPG 204
Query: 63 HGSLLHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINITML 113
HGS L ENTA EK+ + RE + L++N +L IGDVT++N+T L
Sbjct: 205 HGSKLMENTAMEKLEKSVESIRRFRESQFQLLQSNPDLAIGDVTSVNLTKL 255
>gnl|CDD|216562 pfam01546, Peptidase_M20, Peptidase family M20/M25/M40. This
family includes a range of zinc metallopeptidases
belonging to several families in the peptidase
classification. Family M20 are Glutamate
carboxypeptidases. Peptidase family M25 contains X-His
dipeptidases.
Length = 310
Score = 37.5 bits (87), Expect = 6e-04
Identities = 23/110 (20%), Positives = 35/110 (31%), Gaps = 5/110 (4%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEE GG +G + A ++ + + PT + G R + + G G
Sbjct: 69 DEEGGGFEGARALIEDGAIFGLHPDQGV---VGEPTGL-PGGTGIRGSLDLFLTVIGGAG 124
Query: 63 H-GSLLHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINIT 111
H GS H A + L L + IG V +
Sbjct: 125 HHGSPPHGGNAIALAAAALILLLQLIVSRGVDPLDPAVVGIGTVGGGGGS 174
>gnl|CDD|193570 cd08659, M20_ArgE_DapE_like, Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE)-like. Peptidase M20 acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) like family of 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
family are mostly bacterial and have been inferred by
homology as being related to both, ArgE and DapE. This
family also includes N-acetyl-L-citrulline deacetylase
(ACDase; acetylcitrulline deacetylase), a unique, novel
enzyme found in Xanthomonas campestris, a plant
pathogen, in which N-acetyl-L-ornithine is the substrate
for transcarbamoylation reaction, and the product is
N-acetyl-L-citrulline. Thus, in the arginine
biosynthesis pathway, ACDase subsequently catalyzes the
hydrolysis of N-acetyl-L-citrulline to acetate and
L-citrulline.
Length = 365
Score = 36.1 bits (84), Expect = 0.002
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 18/115 (15%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEE G G + + A+ + PT + + ++++ G
Sbjct: 130 DEETGSL-GARALLERGYALR--PDAAI---VGEPTS-LDICIAHKGSLRLRVTATGKAA 182
Query: 63 HGSLLHENTAAEKVN--YIMNKFL-ALREEEKNKLKANKNLTIGDVTTINITMLS 114
HGS VN Y + K + AL E + L G T+N+ ++
Sbjct: 183 HGSRPELG-----VNAIYALAKVIGALEELPFALPAEHPLL--GP-PTLNVGVIK 229
>gnl|CDD|193550 cd05675, M20_yscS_like, M20 Peptidase, carboxypeptidase yscS-like.
Peptidase M20 family, yscS (GlyX-carboxypeptidase, CPS1,
carboxypeptidase S, carboxypeptidase a, carboxypeptidase
yscS, glycine carboxypeptidase)-like subfamily. This
group contains proteins that have been uncharacterized
to date with similarity to vacuolar proteins involved in
nitrogen metabolism which are essential for use of
certain peptides that are sole nitrogen sources. YscS
releases a C-terminal amino acid from a peptide that has
glycine as the penultimate residue. It is synthesized as
one polypeptide chain precursor which yields two active
precursor molecules after carbohydrate modification in
the secretory pathway. The proteolytically unprocessed
forms are associated with the membrane, whereas the
mature forms of the enzyme are soluble. Enzymes in this
subfamily may also cleave intracellularly generated
peptides in order to recycle amino acids for protein
synthesis.
Length = 426
Score = 36.0 bits (84), Expect = 0.002
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 3 DEEIGGSQGMSLFVTT--DAFKKMNVGCALDEG------IASPTEVFALFNGERTIWQMK 54
DEE GG G V D F A++EG ++ + E+ ++
Sbjct: 133 DEEAGGEYGAKWLVENHPDLFD--GAEFAINEGGGGSLDDGGKPRLYPIQTAEKGYAWLR 190
Query: 55 IHCPGTPGHGSLLHENTAAEKV 76
+ G GHGS+ + A ++
Sbjct: 191 LTATGPGGHGSMPRPDNAIYRL 212
>gnl|CDD|181163 PRK07906, PRK07906, hypothetical protein; Provisional.
Length = 426
Score = 34.1 bits (79), Expect = 0.008
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 3 DEEIGGSQGMSLFVTT--DAFKKMNVGC--ALDEG------IASPTEVFALFNGERTIWQ 52
DEE GG+ G V + F+ G A+ E + ++ + E+ +
Sbjct: 138 DEEAGGTYGAHWLVDNHPELFE----GVTEAISEVGGFSLTVPGRDRLYLIETAEKGLAW 193
Query: 53 MKIHCPGTPGHGSLLHENTA 72
M++ G GHGS+++++ A
Sbjct: 194 MRLTARGRAGHGSMVNDDNA 213
>gnl|CDD|233632 TIGR01910, DapE-ArgE, acetylornithine deacetylase or
succinyl-diaminopimelate desuccinylase. This group of
sequences contains annotations for both acetylornithine
deacetylase and succinyl-diaminopimelate desuccinylase,
but does not contain any members with experimental
characterization. Bacillus, Staphylococcus and
Sulfolobus species contain multiple hits to this
subfamily and each may have a separate activity.
Determining which is which must await further laboratory
research [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 375
Score = 33.9 bits (78), Expect = 0.008
Identities = 26/115 (22%), Positives = 38/115 (33%), Gaps = 14/115 (12%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEE G + + L + K G I P+ + G + K+ G
Sbjct: 138 DEESGEAGTLYL--LQRGYFKDADGVL----IPEPSGGDNIVIGHKGSIWFKLRVKGKQA 191
Query: 63 HGSLLHENTAAEKVNYIMN--KFL-ALREEEKNKLKANKNLTIGDVTTINITMLS 114
H S VN IM K + L E E++ N I T N ++
Sbjct: 192 HAS-----FPQFGVNAIMKLAKLITELNELEEHIYARNSYGFIPGPITFNPGVIK 241
>gnl|CDD|223697 COG0624, ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate
desuccinylase and related deacylases [Amino acid
transport and metabolism].
Length = 409
Score = 33.6 bits (77), Expect = 0.012
Identities = 17/114 (14%), Positives = 34/114 (29%), Gaps = 7/114 (6%)
Query: 3 DEEIGGSQGMS--LFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGT 60
DEE G G L +A + E + G + +++ G
Sbjct: 149 DEESG-GAGGKAYLEEGEEALGIRPDYEIVGEPTLESEGGDIIVVGHKGSLWLEVTVKGK 207
Query: 61 PGHGSLLHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINITMLS 114
GH S + ++ + L EE + + +N+ ++
Sbjct: 208 AGHASTTPPDLGRNPIHAAIEALAELIEELGDLAGEGFD----GPLGLNVGLIL 257
>gnl|CDD|219515 pfam07687, M20_dimer, Peptidase dimerisation domain. This domain
consists of 4 beta strands and two alpha helices which
make up the dimerisation surface of members of the M20
family of peptidases. This family includes a range of
zinc metallopeptidases belonging to several families in
the peptidase classification. Family M20 are Glutamate
carboxypeptidases. Peptidase family M25 contains X-His
dipeptidases.
Length = 107
Score = 31.5 bits (72), Expect = 0.031
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 10/71 (14%)
Query: 45 NGERTIWQMKIHCPGTPGHGSLLHENTAAEKVNYIMNKFLA-LREEEKNKLKANKNLTIG 103
G + + K+ G GH + A ++ + LA L E +
Sbjct: 1 IGHKGLAGGKLTVKGKAGHSGAPGKGVNA---IKLLARLLAELPAEYGDIGFDFPR---- 53
Query: 104 DVTTINITMLS 114
TT+NIT +
Sbjct: 54 --TTLNITGIE 62
>gnl|CDD|237268 PRK13013, PRK13013, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 427
Score = 30.9 bits (70), Expect = 0.10
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEE GG G++ F V + I P + G R +W ++ G
Sbjct: 156 DEESGGFGGVAYLAEQGRFSPDRVQHVI---IPEPLNKDRICLGHRGVWWAEVETRGRIA 212
Query: 63 HGSL 66
HGS+
Sbjct: 213 HGSM 216
>gnl|CDD|193559 cd08011, M20_ArgE_DapE_like6, 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 archaeal, and have been inferred by
homology as being related to both ArgE and DapE.
Length = 390
Score = 30.4 bits (69), Expect = 0.14
Identities = 35/120 (29%), Positives = 46/120 (38%), Gaps = 29/120 (24%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEG--------IASPTEVFALFNGERTIWQMK 54
DEE GG G V +EG IA P+ + ++ G R I +
Sbjct: 143 DEESGGETGTGYLV--------------EEGGIRPDYVIIAEPSGLDNIWIGHRGIVWGE 188
Query: 55 IHCPGTPGHGSL--LHENTAAEKVNYIMNKFLALREEEKNKLKANK-NLTIGDVTTINIT 111
+ G HGS L N A EK + I L L+E K +L + K D T N T
Sbjct: 189 VRVKGKQAHGSTPWLGIN-AFEKASVIA---LELQEALKPRLSSRKSKYEYEDERTANPT 244
>gnl|CDD|220808 pfam10558, MTP18, Mitochondrial 18 KDa protein (MTP18). This
family of proteins are mitochondrial 18KDa proteins
that are often misannotated as carbonic anhydrases. It
was shown that knockdown of MTP18 protein results in a
cytochrome c release from mitochondria and consequently
leads to apoptosis. Overexpression studies suggest that
MTP18 is required for mitochondrial fission.
Length = 148
Score = 29.2 bits (66), Expect = 0.33
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 8 GSQGMS-LFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQM 53
S G+S +V D K +EG+ S +A+ +R +WQ
Sbjct: 43 ASYGVSWSYVLGDVSDKGYKAYLKNEGVPSKATDYAVVMVDRAVWQS 89
>gnl|CDD|131269 TIGR02214, spoVD_pbp, stage V sporulation protein D. This model
describes the spoVD subfamily of homologs of the cell
division protein FtsI, a penicillin binding protein.
This subfamily is restricted to Bacillus subtilis and
related Gram-positive species with known or suspected
endospore formation capability. In these species, the
functional equivalent of FtsI is desginated PBP-2B, a
paralog of spoVD [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan,
Cellular processes, Sporulation and germination].
Length = 636
Score = 27.9 bits (62), Expect = 1.1
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 17/79 (21%)
Query: 21 FKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPGHGSL-------------- 66
FK + A++EGI ++ F +G T+ KI C GHGS
Sbjct: 291 FKIITSSAAMEEGIVKESDKFYD-DGSATVGGKKIKCWKPGGHGSQTFPEVVQNSCNPGF 349
Query: 67 --LHENTAAEKVNYIMNKF 83
L AEK+N + F
Sbjct: 350 IELGMRLGAEKLNNYILAF 368
>gnl|CDD|193515 cd03895, M20_ArgE_DapE_like2, 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. 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 have been inferred
by homology as being related to both ArgE and DapE.
Length = 399
Score = 27.1 bits (61), Expect = 1.9
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 49 TIWQMKIHCPGTPGHGSLLHENTAA-EKVNYIMNKFLALREEEKN 92
+W ++ PG P H + +E A EK ++ L E E N
Sbjct: 185 VLW-FRLRVPGRPAHAATRYEGVNAIEKAYALIAALREL-EAEWN 227
>gnl|CDD|236323 PRK08651, PRK08651, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 394
Score = 27.3 bits (61), Expect = 1.9
Identities = 19/95 (20%), Positives = 31/95 (32%), Gaps = 10/95 (10%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPG 62
DEE GG+ L + + P+ + + G R + + G
Sbjct: 144 DEETGGTGTGYLVEEGKVTPDYVI-------VGEPSGLDNICIGHRGLVWGVVKVYGKQA 196
Query: 63 HGSL--LHENTAAEKVNYIMNKFLALREEEKNKLK 95
H S L N A E I + + K+K +
Sbjct: 197 HASTPWLGIN-AFEAAAKIAERLKSSLSTIKSKYE 230
>gnl|CDD|235965 PRK07205, PRK07205, hypothetical protein; Provisional.
Length = 444
Score = 26.6 bits (59), Expect = 3.0
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 33 GIASPTEVFALFNGERTIWQMKIHCPGTP 61
G A P F L E+ + Q K+ PG+
Sbjct: 170 GFA-PDSSFPLTYAEKGLLQAKLVGPGSD 197
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 26.5 bits (59), Expect = 3.3
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 57 CPGTPGHGSLLHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINI 110
G+ G GS +T+ E ++ L R+E ++ KA L D +
Sbjct: 464 VEGSDGLGSQGQNSTS-ENFKPLLEALLRFRDEVRDAAKAEMKLISLDKKKKQL 516
>gnl|CDD|166979 PRK00466, PRK00466, acetyl-lysine deacetylase; Validated.
Length = 346
Score = 26.7 bits (59), Expect = 3.5
Identities = 22/80 (27%), Positives = 28/80 (35%), Gaps = 10/80 (12%)
Query: 3 DEEIGGSQGM-SLFVTTDAFKKMNVGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTP 61
DEE S G L FK + VG P+ + R Q+ I C GTP
Sbjct: 121 DEE-STSIGAKELVSKGFNFKHIIVG--------EPSNGTDIVVEYRGSIQLDIMCEGTP 171
Query: 62 GHGSLLHENTAAEKVNYIMN 81
H S N + I+
Sbjct: 172 EHSSSAKSNLIVDISKKIIE 191
>gnl|CDD|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
cytosolic family. The leucyl-tRNA synthetases belong
to two families so broadly different that they are
represented by separate models. This model includes
both archaeal and cytosolic eukaryotic leucyl-tRNA
synthetases; the eubacterial and mitochondrial forms
differ so substantially that some other tRNA ligases
score higher by this model than does any eubacterial
LeuS [Protein synthesis, tRNA aminoacylation].
Length = 938
Score = 26.7 bits (59), Expect = 3.6
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 39 EVFALF---NGERTIWQMKIHCPGTP 61
EV A F G+ ++ + H GTP
Sbjct: 52 EVSARFERMKGKNVLFPLGFHVTGTP 77
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 26.1 bits (58), Expect = 4.4
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 12/61 (19%)
Query: 26 VGCALDEGIASPTEVFALFNGERTIWQMKIHCPGTPGHGSLLHENTAAEKVNYIMNKFLA 85
VG A GIA+P +V+ L R + I HG H +T I N + A
Sbjct: 158 VGIADTVGIATPRQVYELVRTLRGVVSCDIEF-----HG---HNDTGCA----IANAYAA 205
Query: 86 L 86
L
Sbjct: 206 L 206
>gnl|CDD|130957 TIGR01902, dapE-lys-deAc, N-acetyl-ornithine/N-acetyl-lysine
deacetylase. This clade of mainly archaeal and related
bacterial species contains two characterized enzymes, an
deacetylase with specificity for both N-acetyl-ornithine
and N-acetyl-lysine from Thermus which is found within a
lysine biosynthesis operon, and a fusion protein with
acetyl-glutamate kinase (an enzyme of ornithine
biosynthesis) from Lactobacillus. It is possible that
all of the sequences within this clade have dual
specificity, or that a mix of specificities have evolved
within this clade.
Length = 336
Score = 26.4 bits (58), Expect = 4.5
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 34 IASPTEVFALFNGERTIWQMKIHCPGTPGHGSLLHENTAAEKVNYIMNKFLALREE 89
+ P+ + G + Q+KI C GTP H S N A ++Y + E
Sbjct: 133 VGEPSGAEGITLGYKGSLQLKIMCEGTPFHSS-SAGNAAELLIDY----SKKIIEV 183
>gnl|CDD|239675 cd03704, eRF3c_III, This family represents eEF1alpha-like
C-terminal region of eRF3 homologous to the domain III
of EF-Tu. eRF3 is a GTPase, which enhances the
termination efficiency by stimulating the eRF1 activity
in a GTP-dependent manner. The C-terminal region is
responsible for translation termination activity and is
essential for viability. Saccharomyces cerevisiae eRF3
(Sup35p) is a translation termination factor which is
divided into three regions N, M and a C-terminal
eEF1a-like region essential for translation
termination. Sup35NM is a non-pathogenic prion-like
protein with the property of aggregating into
polymer-like fibrils.
Length = 108
Score = 25.3 bits (56), Expect = 5.3
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 60 TPGHGSLLHENTAAEKVNYIMNKFLALREEEKNKLKANK 98
T G+ ++LH +TA E+V K +AL +++ K +
Sbjct: 21 TAGYSAVLHIHTAVEEVTIK--KLIALIDKKTGKKSKKR 57
>gnl|CDD|239434 cd03318, MLE, Muconate Lactonizing Enzyme (MLE), an homooctameric
enzyme, catalyses the conversion of cis,cis-muconate
(CCM) to muconolactone (ML) in the catechol branch of
the beta-ketoadipate pathway. This pathway is used in
soil microbes to breakdown lignin-derived aromatics,
catechol and protocatechuate, to citric acid cycle
intermediates. Some bacterial species are also capable
of dehalogenating chloroaromatic compounds by the action
of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs
are members of the enolase superfamily characterized by
the presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and that
is stabilized by coordination to the essential Mg2+ ion.
Length = 365
Score = 25.7 bits (57), Expect = 5.7
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 20/77 (25%)
Query: 1 MLDEEIGGSQGMSLFVTTDAFKKMNVGCAL-------DEGIASPTEVFALFNGERTIWQM 53
ML+ IG + LF T + GC L ++ + E A +GE
Sbjct: 298 MLESSIGTAASAHLFAT---LPSLPFGCELFGPLLLAEDLL---EEPLAYRDGE------ 345
Query: 54 KIHCPGTPGHGSLLHEN 70
+H P PG G L E+
Sbjct: 346 -LHVPTGPGLGVRLDED 361
>gnl|CDD|213742 TIGR02827, RNR_anaer_Bdell, anaerobic ribonucleoside-triphosphate
reductase. Members of this family belong to the class
III anaerobic ribonucleoside-triphosphate reductases
(RNR). These glycine-radical-containing enzymes are
oxygen-sensitive and operate under anaerobic conditions.
The genes for this family are pair with genes for an
acitivating protein that creates a glycine radical.
Members of this family, though related, fall outside the
scope of TIGR02487, a functionally equivalent protein
set; no genome has members in both familes.
Identification as RNR is supported by gene pairing with
the activating protein, lack of other anaerobic RNR, and
presence of an upstream regulatory element strongly
conserved upstream of most RNR operons [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 586
Score = 25.5 bits (56), Expect = 7.1
Identities = 11/47 (23%), Positives = 24/47 (51%)
Query: 67 LHENTAAEKVNYIMNKFLALREEEKNKLKANKNLTIGDVTTINITML 113
L E +K+++I A + +K+ AN N+T+ ++ T+ +
Sbjct: 2 LQEEQLGDKLDFIEQYCHAKNAADGSKMDANANVTVKNIATLEAEIS 48
>gnl|CDD|193549 cd05674, M20_yscS, M20 Peptidase, carboxypeptidase yscS. Peptidase
M20 family, yscS (GlyX-carboxypeptidase, CPS1,
carboxypeptidase S, carboxypeptidase a, carboxypeptidase
yscS, glycine carboxypeptidase)-like subfamily. This
group mostly contains proteins that have been
uncharacterized to date, but also includes vacuolar
proteins involved in nitrogen metabolism which are
essential for use of certain peptides that are sole
nitrogen sources. YscS releases a C-terminal amino acid
from a peptide that has glycine as the penultimate
residue. It is synthesized as one polypeptide chain
precursor which yields two active precursor molecules
after carbohydrate modification in the secretory
pathway. The proteolytically unprocessed forms are
associated with the membrane, whereas the mature forms
of the enzyme are soluble. Enzymes in this subfamily
may also cleave intracellularly generated peptides in
order to recycle amino acids for protein synthesis.
Length = 441
Score = 25.2 bits (56), Expect = 8.4
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 16/98 (16%)
Query: 3 DEEIGGSQGMSLFVTTDAFKKMNV--GCALDEG-------IASPTEVFALFN-GERTIWQ 52
DEE+GG++G + + ++ V LDEG AL E+
Sbjct: 143 DEEVGGTRGAAAIA--ELLERYGVDLAFVLDEGGAILEGLFPGVGTPVALIGVAEKGYLD 200
Query: 53 MKIHCPGTPGHGSLLHENTAAEKVNYIMNKFLALREEE 90
+++ G GH S+ +TA I+ + + E+
Sbjct: 201 VRLTVRGPGGHSSMPPPHTAIG----ILAEAITRLEDN 234
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
0.316 0.133 0.383
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,700,222
Number of extensions: 474404
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 390
Number of HSP's successfully gapped: 36
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)