RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16052
(476 letters)
>gnl|CDD|200596 cd10974, CE4_CDA_like_1, Putative catalytic domain of chitin
deacetylase-like proteins with additional chitin-binding
peritrophin-A domain (ChBD) and/or a low-density
lipoprotein receptor class A domain (LDLa). Chitin
deacetylases (CDAs, EC 3.5.1.41) are secreted
metalloproteins belonging to a family of extracellular
chitin-modifying enzymes that catalyze the
N-deacetylation of chitin, a beta-1,4-linked
N-acetylglucosamine polymer, to form chitosan, a polymer
of beta-(1,4)-linked d-glucosamine residues. CDAs have
been isolated and characterized from various bacterial
and fungal species and belong to the larger carbohydrate
esterase 4 (CE4) superfamily. This family includes many
CDA-like proteins mainly from insects, which contain a
putative CDA-like catalytic domain similar to the
catalytic NodB homology domain of CE4 esterases. In
addition to the CDA-like domain, family members contain
two additional domains, a chitin-binding peritrophin-A
domain (ChBD) and a low-density lipoprotein receptor
class A domain (LDLa), or have the ChBD domain but do
not have the LDLa domain.
Length = 269
Score = 504 bits (1301), Expect = e-180
Identities = 193/278 (69%), Positives = 222/278 (79%), Gaps = 10/278 (3%)
Query: 178 PQMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKYTNYSAVQELHRKGH 237
PQMIT+TFDDAIN+NNI LYK++FNGKR NPNGC IK TFFVSH+YTNY AVQ+LHRKGH
Sbjct: 1 PQMITLTFDDAINDNNIELYKKIFNGKRNNPNGCPIKGTFFVSHEYTNYQAVQKLHRKGH 60
Query: 238 EVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRVGGNN 297
E+AVHSITHNDDEN NAT +DW KEM GMR I EK+AN++DN +VG+RAP+LRVGGN
Sbjct: 61 EIAVHSITHNDDEN---NATYEDWVKEMVGMREILEKFANITDNEIVGMRAPFLRVGGNR 117
Query: 298 QFTMMEEQAFLYDSTITAPLSNPPLWPYTMYFRMPHRCHGNLQHCPTRS-HAVWEMVMNE 356
QF MMEE FLYDS+ITAP SN PLWPYT+ ++MPH CHG Q+CPTRS VWEMV+NE
Sbjct: 118 QFEMMEEFGFLYDSSITAPPSNVPLWPYTLDYKMPHECHG--QNCPTRSFPGVWEMVLNE 175
Query: 357 LDRREDPNFDEYLPGCAMVDSCSNILTGDQFYNFLNHNFDRHYDQNRAPLGLYFHAAWLK 416
LD R+DP DE L AM DSC NIL+GDQ Y +L HNF+RHY NRAP GLYFH WLK
Sbjct: 176 LDVRDDPQGDEPL---AMDDSCLNILSGDQVYEWLQHNFERHYLTNRAPYGLYFHTNWLK 232
Query: 417 NNPEFLDAFLYWVDEIIERHKDVYFVTMTQVIQWIQNP 454
E L A ++DEI++ DVYFVTMTQ IQW+QNP
Sbjct: 233 TKNELLRALQKFLDEILQ-LPDVYFVTMTQAIQWMQNP 269
>gnl|CDD|200597 cd10975, CE4_CDA_like_2, Putative catalytic domain of chitin
deacetylase-like proteins. Chitin deacetylases (CDAs,
EC 3.5.1.41) are secreted metalloproteins belonging to a
family of extracellular chitin-modifying enzymes that
catalyze the N-deacetylation of chitin, a
beta-1,4-linked N-acetylglucosamine polymer, to form
chitosan, a polymer of beta-(1,4)-linked d-glucosamine
residues. CDAs have been isolated and characterized from
various bacterial and fungal species and belong to the
larger carbohydrate esterase 4 (CE4) superfamily. This
family includes many midgut-specific CDA-like proteins
mainly from insects, such as Tribolium castaneum CDAs
(TcCDA6-9). These proteins contain a putative CDA-like
catalytic domain similar to the catalytic NodB homology
domain of CE4 esterases. In addition to the CDA-like
domain, some family members have an additional
chitin-binding peritrophin-A domain (ChBD).
Length = 268
Score = 314 bits (806), Expect = e-105
Identities = 120/279 (43%), Positives = 178/279 (63%), Gaps = 13/279 (4%)
Query: 178 PQMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKYTNYSAVQELHRKGH 237
PQ++T+TFDDA+N N Y+++F RKNPNGC I ATFFVSH+YT+Y VQEL+ GH
Sbjct: 1 PQLVTLTFDDAVNTLNYPYYEKLFGN-RKNPNGCPIGATFFVSHEYTDYRLVQELYNDGH 59
Query: 238 EVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRVGGNN 297
E+A+HSI+H +++W NA+VD+W +E G R I +AN+ + G RAP+L++GG+
Sbjct: 60 EIALHSISHRSPQDYWRNASVDEWEREFGGQREILAHFANIPAEDIKGFRAPFLQLGGDA 119
Query: 298 QFTMMEEQAFLYDST-ITAPLSNPPLWPYTMYFRMPHRCHGNLQHCPTRSHA-VWEMVMN 355
F +++ YDS+ T +NPPLWPYT+ + C + CPT S+ W + M
Sbjct: 120 TFKALKQLGLTYDSSWPTQSFTNPPLWPYTLDYGSTQDC--VIPPCPTDSYPGFWVVPMV 177
Query: 356 ELDRREDPNFDEYLPGCAMVDSCSNILTGDQFYNFLNHNFDRHYDQNRAPLGLYFHAAWL 415
+ +D N C+M+ +C T D+ Y++L NF+RHY+ NRAP GLY HA+W
Sbjct: 178 DW---QDLN----GVPCSMLAACPPPGTADEVYDWLLSNFERHYNTNRAPFGLYLHASWF 230
Query: 416 KNNPEFLDAFLYWVDEIIERHKDVYFVTMTQVIQWIQNP 454
+ P L+ F ++DE++ DVY VT++Q I+W++NP
Sbjct: 231 EFTPNRLEGFKKFLDELLS-LDDVYLVTISQAIEWMRNP 268
>gnl|CDD|200545 cd10919, CE4_CDA_like, Putative catalytic domain of chitin
deacetylase-like proteins from insects and similar
proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are
secreted metalloproteins belonging to a family of
extracellular chitin-modifying enzymes that catalyze the
N-deacetylation of chitin, a beta-1,4-linked
N-acetylglucosamine polymer, to form chitosan, a polymer
of beta-(1,4)-linked d-glucosamine residues. CDAs have
been isolated and characterized from various bacterial
and fungal species and belong to the larger carbohydrate
esterase family 4 (CE4). This family includes many
CDA-like proteins, mainly from insects, which contain a
putative CDA-like catalytic domain similar to the
catalytic NodB homology domain of CE4 esterases. Some
family members have an additional chitin binding domain
(ChBD), or an additional low-density lipoprotein
receptor class A domain (LDLa), or both. Due to the lack
of some catalytically relevant residues, several insect
CDA-like proteins are devoid of enzymatic activity and
may simply bind to chitin and thus influence the
mechanical or permeability properties of
chitin-containing structures such as the cuticle or the
peritrophic membrane. This family also includes many
uncharacterized hypothetical proteins from bacteria,
exhibiting high sequence similarity to insect CDA-like
proteins.
Length = 273
Score = 311 bits (800), Expect = e-104
Identities = 117/284 (41%), Positives = 156/284 (54%), Gaps = 18/284 (6%)
Query: 178 PQMITITFDDAINN-NNIALYKEMFNGKRKNPNGCDIKATFFVSHKYTNYSAVQELHRKG 236
PQ + TFDDAIN N A+ +E+ +G N GC I ATFFVS YT+ S V++L R+G
Sbjct: 1 PQFVLFTFDDAINELNTDAVIQEIADG-TNNNGGCPIPATFFVSTNYTDCSLVKQLWREG 59
Query: 237 HEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRVGGN 296
HE+A H++TH D+ SNA+VD+W +E+AG R K + VVG RAPYL
Sbjct: 60 HEIATHTVTHVPDD---SNASVDEWEEEIAGQREWLNKTCGIPLEKVVGFRAPYL-AYNP 115
Query: 297 NQFTMMEEQAFLYDSTITAPL---SNPPLWPYTMYFRMPHRCHGNLQHC--PTRSHAVWE 351
N ++EE FLYDS+I P LWPYT+ + +P C+ C R +WE
Sbjct: 116 NTREVLEENGFLYDSSIPEPYTPSGTNRLWPYTLDYGIPQDCNLVPGSCSPTERYPGLWE 175
Query: 352 MVMNELDRREDPNFDEYLPGCAMVDSCSNILTGDQFYNFLNHNFDRHYDQNRAPLGLYFH 411
+ + L D D Y L GD FY L +NFDRHY+ NRAP G+Y H
Sbjct: 176 VPLYTLQDGNDTTGDSY-----YCTPDDGPLNGDSFYALLKYNFDRHYNGNRAPFGIYLH 230
Query: 412 AAWLKN-NPEFLDAFLYWVDEIIERHKDVYFVTMTQVIQWIQNP 454
AAWL E A ++D + DV+FVT +Q++ W+QNP
Sbjct: 231 AAWLSPPYSERRAALEKFLDYALS-KPDVWFVTNSQLLDWMQNP 273
>gnl|CDD|200598 cd10976, CE4_CDA_like_3, Putative catalytic domain of
uncharacterized bacterial hypothetical proteins similar
to insect chitin deacetylase-like proteins. The family
includes many uncharacterized bacterial hypothetical
proteins that show high sequence similarity to insect
chitin deacetylase-like proteins. Chitin deacetylases
(CDAs, EC 3.5.1.41) are secreted metalloproteins
belonging to a family of extracellular chitin-modifying
enzymes that catalyze the N-deacetylation of chitin, a
beta-1,4-linked N-acetylglucosamine polymer, to form
chitosan, a polymer of beta-(1,4)-linked d-glucosamine
residues.
Length = 299
Score = 63.9 bits (156), Expect = 3e-11
Identities = 57/246 (23%), Positives = 93/246 (37%), Gaps = 50/246 (20%)
Query: 233 HRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGM-RIIAEKYAN-----------LSD 280
+R+GHE+ H+ H D + +V DW +E R + YA +
Sbjct: 82 YREGHEIGSHANGHFDGKGGGGRWSVADWKREFDQFYRFVENAYAINGIEGAPPWPAFAP 141
Query: 281 NSVVGVRAPYLRVGGNNQFTMMEEQAFLYDSTITAPLSNPPLWPYTM----YFRMPHRCH 336
NS+ G RAP L Q +++ F YD++ ++ P WP + F +P
Sbjct: 142 NSIKGFRAPCLEGSKGLQPA-LKKHGFTYDAS---SVTQGPYWPQKVDGIWNFPLP---- 193
Query: 337 GNLQHCPTRSHAVWEMVMNELDR----REDP-NFDEYLPGCAMVDSCSNILTGDQFYNFL 391
L S V M N R E P E+ +
Sbjct: 194 --LVPEGPTSRPVIAMDYNLFVRHSGGVEAPAKAAEF---------------EARMLATY 236
Query: 392 NHNFDRHYDQNRAPLGLYFH-AAWLKNNPEFLDAFLYWVDEIIERHKDVYFVTMTQVIQW 450
+ FDR Y+ NRAPL L H W N + +A + +E+ + +V VT +++ +
Sbjct: 237 RNAFDRAYNGNRAPLQLGNHFVKW--NGGAYWNALERFAEEVCTK-PEVKCVTYRELVDF 293
Query: 451 IQNPRT 456
++
Sbjct: 294 LEAQDP 299
>gnl|CDD|216550 pfam01522, Polysacc_deac_1, Polysaccharide deacetylase. This
domain is found in polysaccharide deacetylase. This
family of polysaccharide deacetylases includes NodB
(nodulation protein B from Rhizobium) which is a
chitooligosaccharide deacetylase. It also includes
chitin deacetylase from yeast, and endoxylanases which
hydrolyses glucosidic bonds in xylan.
Length = 124
Score = 57.6 bits (140), Expect = 2e-10
Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 17/113 (15%)
Query: 180 MITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYTNYSAVQELHRKGH 237
+ +TFDD +N + + +K +KATFFV + T V+ + +GH
Sbjct: 8 SVALTFDDGPPDNTPRILDVL----KKY----GVKATFFVIGGNAETYPDLVRRMVAEGH 59
Query: 238 EVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPY 290
E+ H+ +H D S + E+ + +K R PY
Sbjct: 60 EIGNHTWSHP-DLTALSPEEIR---AEILRSQEAIKKATG---KRPRLFRPPY 105
>gnl|CDD|238060 cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a
cysteine-rich repeat that plays a central role in
mammalian cholesterol metabolism; the receptor protein
binds LDL and transports it into cells by endocytosis; 7
successive cysteine-rich repeats of about 40 amino acids
are present in the N-terminal of this multidomain
membrane protein; other homologous domains occur in
related receptors, including the very low-density
lipoprotein receptor and the LDL receptor-related
protein/alpha 2-macroglobulin receptor, and in proteins
which are functionally unrelated, such as the C9
component of complement; the binding of calcium is
required for in vitro formation of the native disulfide
isomer and is necessary in establishing and maintaining
the modular structure.
Length = 35
Score = 51.8 bits (125), Expect = 3e-09
Identities = 16/35 (45%), Positives = 18/35 (51%)
Query: 103 CQDGFLACGDGACIERGLFCNGEKDCNDGSDENTC 137
C C +G CI C+GE DC DGSDE C
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEENC 35
>gnl|CDD|213020 cd10585, CE4_SF, Catalytic NodB homology domain of the carbohydrate
esterase 4 superfamily. The carbohydrate esterase 4
(CE4) superfamily mainly includes chitin deacetylases
(EC 3.5.1.41), bacterial peptidoglycan
N-acetylglucosamine deacetylases (EC 3.5.1.-), and
acetylxylan esterases (EC 3.1.1.72), which catalyze the
N- or O-deacetylation of substrates such as acetylated
chitin, peptidoglycan, and acetylated xylan,
respectively. Members in this superfamily contain a NodB
homology domain that adopts a deformed (beta/alpha)8
barrel fold, which encompasses a mononuclear
metalloenzyme employing a conserved His-His-Asp
zinc-binding triad, closely associated with the
conserved catalytic base (aspartic acid) and acid
(histidine) to carry out acid/base catalysis. The NodB
homology domain of CE4 superfamily is remotely related
to the 7-stranded beta/alpha barrel catalytic domain of
the superfamily consisting of family 38 glycoside
hydrolases (GH38), family 57 heat stable retaining
glycoside hydrolases (GH57), lactam utilization protein
LamB/YcsF family proteins, and YdjC-family proteins.
Length = 142
Score = 53.2 bits (128), Expect = 1e-08
Identities = 30/150 (20%), Positives = 52/150 (34%), Gaps = 29/150 (19%)
Query: 180 MITITFDDAINNNNIALY----KEMFNGKRKNPNGCDIKATFFVSHKY----------TN 225
++ +T DD ++ G I AT FV N
Sbjct: 1 LVLLTLDDDPAFEGSPAALQRLLDLLEGYG-------IPATLFVIPGNANPDKLMKSPLN 53
Query: 226 YSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVG 285
+ ++EL GHE+ +H TH D + ++ +++ R I E+ G
Sbjct: 54 WDLLRELLAYGHEIGLHGYTHPDLAYGNLSP--EEVLEDLLRARRILEEAGGQ---PPKG 108
Query: 286 VRAPYLRVGGNNQFTMMEE-QAFLYDSTIT 314
RAP + + ++E YDS +
Sbjct: 109 FRAPGGNL--SETVKALKELGDIQYDSDLA 136
>gnl|CDD|200589 cd10967, CE4_GLA_like_6s, Putative catalytic NodB homology domain
of gellan lyase and similar proteins. This family is
represented by the extracellular
polysaccharide-degrading enzyme, gellan lyase
(gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme
acts on gellan exolytically and releases a
tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose
with unsaturated glucuronic acid at the nonreducing
terminus. The family also includes many uncharacterized
prokaryotic polysaccharide deacetylases, which show high
sequence similarity to Bacillus sp. gellan lyase.
Although their biological functions remain unknown, all
members of the family contain a conserved domain with a
6-stranded beta/alpha barrel, which is similar to the
catalytic NodB homology domain of rhizobial NodB-like
proteins, belonging to the larger carbohydrate esterase
4 (CE4) superfamily.
Length = 202
Score = 53.9 bits (130), Expect = 2e-08
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 180 MITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVS------HKYTNYSAVQELH 233
+++TFDD + A + K +K TFFV+ Y + ++EL
Sbjct: 2 AVSLTFDDGYAQDLRAA--PLLA-KY------GLKGTFFVNSGLLGRRGYLDLEELRELA 52
Query: 234 RKGHEVAVHSITHND 248
GHE+ H++TH D
Sbjct: 53 AAGHEIGSHTVTHPD 67
>gnl|CDD|200578 cd10954, CE4_CtAXE_like, Catalytic NodB homology domain of
Clostridium thermocellum acetylxylan esterase and its
bacterial homologs. This family is represented by
Clostridium thermocellum acetylxylan esterase (CtAXE, EC
3.1.1.72), a member of the carbohydrate esterase 4 (CE4)
superfamily. CtAXE deacetylates O-acetylated xylan, a
key component of plant cell walls. It shows no
detectable activity on generic esterase substrates
including para-nitrophenyl acetate. It is specific for
sugar-based substrates and will precipitate acetylxylan,
as a consequence of deacetylation. CtAXE is a monomeric
protein containing a catalytic NodB homology domain with
the same overall topology and a deformed (beta/alpha)8
barrel fold as other CE4 esterases. However, due to
differences in the topography of the substrate-binding
groove, the chemistry of the active center, and metal
ion coordination, CtAXE has different metal ion
preference and lacks activity on N-acetyl substrates. It
is significantly activated by Co2+. Moreover, CtAXE
displays distinctly different ligand coordination to the
metal ion, utilizing an aspartate, a histidine, and four
water molecules, as opposed to the conserved His-His-Asp
zinc-binding triad of other CE4 esterases.
Length = 180
Score = 52.6 bits (127), Expect = 4e-08
Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 16/119 (13%)
Query: 180 MITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKYTNYSA--VQELHRKGH 237
M+ +TFDD N ++ K +++ATFF+ + N + V+ + G
Sbjct: 2 MVALTFDDGPNAKYTPRLLDVLE---KY----NVRATFFLVGQNVNGNKEIVKRMVEMGC 54
Query: 238 EVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRVGGN 296
E+ HS TH D + + + KE+ E ++ R PY V
Sbjct: 55 EIGNHSYTHPDL----TKLSPSEIKKEIEKTN---EAIKKITGKRPKLFRPPYGAVNDT 106
>gnl|CDD|216601 pfam01607, CBM_14, Chitin binding Peritrophin-A domain. This
domain is called the Peritrophin-A domain and is found
in chitin binding proteins particularly peritrophic
matrix proteins of insects and animal chitinases.
Copies of the domain are also found in some
baculoviruses. Relevant references that describe
proteins with this domain include. It is an
extracellular domain that contains six conserved
cysteines that probably form three disulphide bridges.
Chitin binding has been demonstrated for a protein
containing only two of these domains.
Length = 53
Score = 48.2 bits (115), Expect = 9e-08
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 26 CKDKDAGEWFRLVAGEGDNCRDVIQCTSSGLQAIRCPAGLYFDIEKQTCDWKGAVKNC 83
C+ + G + +C QC++ CPAGL FD TCD+ V +C
Sbjct: 1 CEGRPDGLYPD-----PGDCSKYYQCSNGKAVVFTCPAGLVFDPALGTCDYPDNVVDC 53
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 46.5 bits (111), Expect = 3e-07
Identities = 16/35 (45%), Positives = 18/35 (51%)
Query: 103 CQDGFLACGDGACIERGLFCNGEKDCNDGSDENTC 137
C CG G CI C+G+ DC DGSDE C
Sbjct: 3 CGPDEFQCGSGECIPMSWVCDGDPDCEDGSDEKNC 37
>gnl|CDD|200566 cd10941, CE4_PuuE_HpPgdA_like_2, Putative catalytic domain of
uncharacterized prokaryotic polysaccharide deacetylases
similar to bacterial PuuE allantoinases and Helicobacter
pylori peptidoglycan deacetylase (HpPgdA). This family
contains many uncharacterized prokaryotic polysaccharide
deacetylases (DCAs) that show high sequence similarity
to the catalytic domain of bacterial PuuE allantoinases
and Helicobacter pylori peptidoglycan deacetylase
(HpPgdA). PuuE allantoinase appears to be
metal-independent and specifically catalyzes the
hydrolysis of (S)-allantoin into allantoic acid.
Different from PuuE allantoinase, HpPgdA has the ability
to bind a metal ion at the active site and is
responsible for a peptidoglycan modification that
counteracts the host immune response. Both PuuE
allantoinase and HpPgdA function as homotetramers. The
monomer is composed of a 7-stranded barrel with
detectable sequence similarity to the 6-stranded barrel
NodB homology domain of DCA-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. In contrast to
typical NodB-like DCAs, PuuE allantoinase and HpPgdA do
not exhibit a solvent-accessible polysaccharide binding
groove and might only bind a small molecule at the
active site.
Length = 258
Score = 51.1 bits (123), Expect = 3e-07
Identities = 29/146 (19%), Positives = 50/146 (34%), Gaps = 24/146 (16%)
Query: 212 DIKATFF----VSHKYTNYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAG 267
+KATFF V+ +Y ++ + GHE+A H H + +D +
Sbjct: 45 GVKATFFVLGEVAERYP--DLIRRIAEAGHEIASHGYAHERVDRLTPEEFREDLRRS--- 99
Query: 268 MRIIAEKYANLSDNSVVGVRAPYLRVGGNNQ-FTMMEEQAFLYDSTITAPLSNPPLWPYT 326
+ +++ VVG RAP + ++ E +LYDS++ P P
Sbjct: 100 ----KKILEDITGQKVVGFRAPNFSI--TPWALDILAEAGYLYDSSV-FPTKRPGYGGPL 152
Query: 327 MYFRMPHRCHGNLQHCPTRSHAVWEM 352
P + E
Sbjct: 153 APKSEPLP-------PIRAKGGILEF 171
>gnl|CDD|197566 smart00192, LDLa, Low-density lipoprotein receptor domain class A.
Cysteine-rich repeat in the low-density lipoprotein
(LDL) receptor that plays a central role in mammalian
cholesterol metabolism. The N-terminal type A repeats in
LDL receptor bind the lipoproteins. Other homologous
domains occur in related receptors, including the very
low-density lipoprotein receptor and the LDL
receptor-related protein/alpha 2-macroglobulin receptor,
and in proteins which are functionally unrelated, such
as the C9 component of complement. Mutations in the LDL
receptor gene cause familial hypercholesterolemia.
Length = 33
Score = 44.9 bits (107), Expect = 9e-07
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 103 CQDGFLACGDGACIERGLFCNGEKDCNDGSDE 134
C G C +G CI C+G DC DGSDE
Sbjct: 2 CPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
>gnl|CDD|213022 cd10917, CE4_NodB_like_6s_7s, Catalytic NodB homology domain of
rhizobial NodB-like proteins. This family belongs to
the large and functionally diverse carbohydrate esterase
4 (CE4) superfamily, whose members show strong sequence
similarity with some variability due to their distinct
carbohydrate substrates. It includes many rhizobial NodB
chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like
proteins, mainly from bacteria and eukaryotes, such as
chitin deacetylases (EC 3.5.1.41), bacterial
peptidoglycan N-acetylglucosamine deacetylases (EC
3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which
catalyze the N- or O-deacetylation of substrates such as
acetylated chitin, peptidoglycan, and acetylated xylan.
All members of this family contain a catalytic NodB
homology domain with the same overall topology and a
deformed (beta/alpha)8 barrel fold with 6- or 7 strands.
Their catalytic activity is dependent on the presence of
a divalent cation, preferably cobalt or zinc, and they
employ a conserved His-His-Asp zinc-binding triad
closely associated with the conserved catalytic base
(aspartic acid) and acid (histidine) to carry out
acid/base catalysis. Several family members show
diversity both in metal ion specificities and in the
residues that coordinate the metal.
Length = 171
Score = 48.4 bits (116), Expect = 1e-06
Identities = 24/115 (20%), Positives = 44/115 (38%), Gaps = 23/115 (20%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKY--TNYSAVQELHRKGHE 238
+ +TFDD + ++ + +KATFFV + + V+ + +GHE
Sbjct: 3 VALTFDDGPDPEYTPKILDIL---AEY----GVKATFFVVGENVEKHPDLVRRIVAEGHE 55
Query: 239 VAVHSITHNDDENFWSNATVDDWAKEMAGM-RIIAEKYANLSDNSVVGVRAPYLR 292
+ H+ +H D + + ++ E+ I E GVR R
Sbjct: 56 IGNHTYSHPD----LTKLSPEEIRAEIERTQDAIEEAT---------GVRPRLFR 97
>gnl|CDD|213757 TIGR03006, pepcterm_polyde, polysaccharide deacetylase family
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
deacetylases (pfam01522). All are found in species that
encode the PEP-CTERM/exosortase system predicted to act
in protein sorting in a number of Gram-negative
bacteria, and are found near the epsH homolog that is
the putative exosortase gene. The highest scoring
homologs below the trusted cutoff for this model are
found in several species of Methanosarcina, an archaeal
genus [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 272
Score = 48.5 bits (116), Expect = 2e-06
Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 15/108 (13%)
Query: 212 DIKATFF----VSHKYTNYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAG 267
+KATFF V+ +Y V+ + GHE+A H H E + T + + ++
Sbjct: 47 GVKATFFTLGWVAERYPEL--VRRIVAAGHELASHGYGH---ERVTTQ-TPEAFRADIRR 100
Query: 268 MRIIAEKYANLSDNSVVGVRAPYLRVGGNN--QFTMMEEQAFLYDSTI 313
+ + E +LS V G RAP +G N ++ E + Y S+I
Sbjct: 101 SKALLE---DLSGQPVRGYRAPSFSIGKKNLWALDVLAEAGYRYSSSI 145
>gnl|CDD|200569 cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of
Streptococcus mutans polysaccharide deacetylase PgdA,
Bacillus subtilis YheN, and similar proteins. This
family is represented by a putative polysaccharide
deacetylase PgdA from the oral pathogen Streptococcus
mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN),
which are members of the carbohydrate esterase 4 (CE4)
superfamily. SmPgdA is an extracellular metal-dependent
polysaccharide deacetylase with a typical CE4 fold, with
metal bound to a His-His-Asp triad. It possesses
de-N-acetylase activity toward a hexamer of
chitooligosaccharide N-acetylglucosamine, but not
shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. SmPgdA plays a role in
tuning cell surface properties and in interactions with
(salivary) agglutinin, an essential component of the
innate immune system, most likely through deacetylation
of an as-yet-unidentified polysaccharide. SmPgdA shows
significant homology to the catalytic domains of
peptidoglycan deacetylases from Streptococcus pneumoniae
(SpPgdA) and Listeria monocytogenes (LmPgdA), both of
which are involved in the bacterial defense mechanism
against human mucosal lysozyme. The Bacillus subtilis
genome contains six polysaccharide deacetylase gene
homologs: pdaA, pdaB (previously known as ybaN), yheN,
yjeA, yxkH and ylxY. The biological function of BsYheN
is still unknown. This family also includes many
uncharacterized polysaccharide deacetylases mainly found
in bacteria.
Length = 189
Score = 46.4 bits (111), Expect = 7e-06
Identities = 31/131 (23%), Positives = 53/131 (40%), Gaps = 34/131 (25%)
Query: 184 TFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYTNYSAVQELHRKGHEVAV 241
TFDD + N + + K+ N +KATFFV S+ V+ + ++GH + +
Sbjct: 6 TFDDGPSKNTPKILDIL---KKYN-----VKATFFVIGSNVEKYPELVKRIVKEGHAIGL 57
Query: 242 HSITHN------DDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRV-G 294
HS TH+ E F D K ++ + GV+ +R G
Sbjct: 58 HSYTHDYKKLYSSPEAFI-----KDLNKTQDLIK------------KITGVKTKLIRFPG 100
Query: 295 GNNQFTMMEEQ 305
G++ +M+
Sbjct: 101 GSSNTGLMKAL 111
>gnl|CDD|200563 cd10938, CE4_HpPgdA_like, Catalytic domain of Helicobacter pylori
peptidoglycan deacetylase (HpPgdA) and similar proteins.
This family is represented by a peptidoglycan
deacetylase (HP0310, HpPgdA) from the gram-negative
pathogen Helicobacter pylori. HpPgdA has the ability to
bind a metal ion at the active site and is responsible
for a peptidoglycan modification that counteracts the
host immune response. It functions as a homotetramer.
The monomer is composed of a 7-stranded barrel with
detectable sequence similarity to the 6-stranded barrel
NodB homology domain of polysaccharide deacetylase
(DCA)-like proteins in the CE4 superfamily, which
removes N-linked or O-linked acetyl groups from cell
wall polysaccharides. In contrast to typical NodB-like
DCAs, HpPgdA does not exhibit a solvent-accessible
polysaccharide binding groove, suggesting that the
enzyme binds a small molecule at the active site.
Length = 258
Score = 46.8 bits (112), Expect = 8e-06
Identities = 30/104 (28%), Positives = 43/104 (41%), Gaps = 14/104 (13%)
Query: 212 DIKATFFVS----HKYTNYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAG 267
D+KATFFV + AV+ + GHE+ H H EN T ++ + +
Sbjct: 50 DVKATFFVPGHTAETFPE--AVEAILAAGHEIGHHGYLH---ENPT-GLTPEEERELLER 103
Query: 268 MRIIAEKYANLSDNSVVGVRAPYLRVGGNNQFTMMEEQAFLYDS 311
E L+ VG R+P N ++ E FLYDS
Sbjct: 104 G---LELLEKLTGKRPVGYRSPSWEF-SPNTLDLLLEHGFLYDS 143
>gnl|CDD|213021 cd10916, CE4_PuuE_HpPgdA_like, Catalytic domain of bacterial PuuE
allantoinases, Helicobacter pylori peptidoglycan
deacetylase (HpPgdA), and similar proteins. This family
is a member of the very large and functionally diverse
carbohydrate esterase 4 (CE4) superfamily. It contains
bacterial PuuE (purine utilization E) allantoinases, a
peptidoglycan deacetylase from Helicobacter pylori
(HpPgdA), Escherichia coli ArnD, and many
uncharacterized homologs from all three kingdoms of
life. PuuE allantoinase appears to be metal-independent
and specifically catalyzes the hydrolysis of
(S)-allantoin into allantoic acid. Different from PuuE
allantoinase, HpPgdA has the ability to bind a metal ion
at the active site and is responsible for a
peptidoglycan modification that counteracts the host
immune response. Both PuuE allantoinase and HpPgdA
function as a homotetramer. The monomer is composed of a
7-stranded barrel with detectable sequence similarity to
the 6-stranded barrel NodB homology domain of
polysaccharide deacetylase (DCA)-like proteins in the
CE4 superfamily, which removes N-linked or O-linked
acetyl groups from cell wall polysaccharides. However,
in contrast with the typical DCAs, PuuE allantoinase and
HpPgdA might not exhibit a solvent-accessible
polysaccharide binding groove and only recognize a small
substrate molecule. ArnD catalyzes the deformylation of
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol.
Length = 247
Score = 44.6 bits (106), Expect = 4e-05
Identities = 49/245 (20%), Positives = 77/245 (31%), Gaps = 52/245 (21%)
Query: 212 DIKATFFVSHKY--TNYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMA-GM 268
++ATFFV + AV+ + GHE+A H H D + + + + +
Sbjct: 49 GVRATFFVPGRVAERFPDAVRAIVAAGHEIAAHGYAHED----VLALSREQEREVLLRSL 104
Query: 269 RIIAEKYANLSDNSVVGVRAPYLRVGGNNQFTMMEEQAFLYDSTITAPLSNPPLWPYTMY 328
++ E L+ G R+P L + ++ E +LYD P W
Sbjct: 105 ELLEE----LTGQRPTGWRSPGLT-FSPDTLELLAELGYLYDGDTY-DDDLPYYWRD--- 155
Query: 329 FRMPHRCHGNLQHCPTRSHAVWEMVMNELDRREDPNFDEYLPGCAMVDSCSNILTGDQFY 388
T + E+ D F G FY
Sbjct: 156 --------------ATGGGPILELPYT--TVLNDLRFFMGGGG-----------LPRAFY 188
Query: 389 NFLNHNFDRHYDQNRAPLGLYFHAAWLKNNP---EFLDAFLYWVDEIIERHKDVYFVTMT 445
FD Y L L H + P LD FL ++ H DV+F T
Sbjct: 189 ENWKEQFDVLY-ARGRYLSLTLH-PRVIGRPARAAALDRFL----RYVKSHPDVWFATHD 242
Query: 446 QVIQW 450
++ +
Sbjct: 243 EIARH 247
>gnl|CDD|214696 smart00494, ChtBD2, Chitin-binding domain type 2.
Length = 49
Score = 40.5 bits (95), Expect = 4e-05
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 42 GDNCRDVIQCTSSGLQAIRCPAGLYFDIEKQTCDWK 77
+C QC++ CPAGL F+ QTCDW
Sbjct: 14 PTDCSKYYQCSNGRPIVGSCPAGLVFNPATQTCDWP 49
>gnl|CDD|200575 cd10951, CE4_ClCDA_like, Catalytic NodB homology domain of
Colletotrichum lindemuthianum chitin deacetylase and
similar proteins. This family is represented by the
chitin deacetylase (endo-chitin de-N-acetylase, ClCDA,
EC 3.5.1.41) from Colletotrichum lindemuthianum (also
known as Glomerella lindemuthiana), which is a member of
the carbohydrate esterase 4 (CE4) superfamily. ClCDA
catalyzes the hydrolysis of N-acetamido groups of
N-acetyl-D-glucosamine residues in chitin, converting it
to chitosan in fungal cell walls. It consists of a
single catalytic domain similar to the deformed
(alpha/beta)8 barrel fold adopted by other CE4
esterases, which encompasses a mononuclear metalloenzyme
employing a conserved His-His-Asp zinc-binding triad
closely associated with the conserved catalytic base
(aspartic acid) and acid (histidine), to carry out
acid/base catalysis. It possesses a highly conserved
substrate-binding groove, with subtle alterations that
influence substrate specificity and subsite affinity.
Unlike its bacterial homologs, ClCDA contains two
intramolecular disulfide bonds that may add stability to
this secreted protein. The family also includes many
uncharacterized deacetylases and hypothetical proteins
mainly from eukaryotes, which show high sequence
similarity to ClCDA.
Length = 197
Score = 43.4 bits (103), Expect = 6e-05
Identities = 30/138 (21%), Positives = 50/138 (36%), Gaps = 31/138 (22%)
Query: 177 VPQMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKYTNY------SAVQ 230
VP + +TFDD + L + K KATFFV+ N ++
Sbjct: 6 VPGTVALTFDDGPSTYTPQLLDLL---KEAG-----AKATFFVNGNNFNGCIYDYADVLR 57
Query: 231 ELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGV---- 286
++ +GH++A H+ +H D + + EM + K ++GV
Sbjct: 58 RMYNEGHQIASHTWSHPD----LTKLSAAQIRDEMTKLEDALRK--------ILGVKPTY 105
Query: 287 -RAPYLRVGGNNQFTMME 303
R PY + E
Sbjct: 106 MRPPYGECNDEVLAVLGE 123
>gnl|CDD|223798 COG0726, CDA1, Predicted xylanase/chitin deacetylase [Carbohydrate
transport and metabolism].
Length = 267
Score = 43.1 bits (101), Expect = 2e-04
Identities = 34/129 (26%), Positives = 52/129 (40%), Gaps = 20/129 (15%)
Query: 167 YIPGDLPSKEVPQMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYT 224
G+LP K + +TFDD + N + +K IKATFFV S
Sbjct: 57 EKKGNLPGK----AVALTFDDGPLDGN---TPRILPLLKKY----GIKATFFVVGSWIER 105
Query: 225 NYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVV 284
N V+ + GHE+ H H D + ++++ E+A I +K ++
Sbjct: 106 NPDLVKRIAEAGHEIGNHGYDHPD----LQDLSLEELGAEIARAHDILKK---ITGGRPR 158
Query: 285 GVRAPYLRV 293
G R PY
Sbjct: 159 GFRPPYGSY 167
>gnl|CDD|234001 TIGR02764, spore_ybaN_pdaB, polysaccharide deacetylase family
sporulation protein PdaB. This model describes the YbaN
protein family, also called PdaB and SpoVIE, of
Gram-positive bacteria. Although ybaN null mutants have
only a mild sporulation defect, ybaN/ytrI double mutants
show drastically reducted sporulation efficiencies. This
synthetic defect suggests the role of this
sigmaE-controlled gene in sporulation had been masked by
functional redundancy. Members of this family are
homologous to a characterized polysaccharide
deacetylase; the exact function this protein family is
unknown [Cellular processes, Sporulation and
germination].
Length = 191
Score = 41.6 bits (98), Expect = 3e-04
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 9/70 (12%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKY--TNYSAVQELHRKGHE 238
I +TFD + N+ + + + ++ D+KATFF+S + + V+E+ + GHE
Sbjct: 8 IALTFDISWGNDY---TEPILDTLKEY----DVKATFFLSGSWAERHPELVKEIVKDGHE 60
Query: 239 VAVHSITHND 248
+ H H +
Sbjct: 61 IGSHGYRHKN 70
>gnl|CDD|200574 cd10950, CE4_BsYlxY_like, Putative catalytic NodB homology domain
of uncharacterized protein YlxY from Bacillus subtilis
and its bacterial homologs. The Bacillus subtilis
genome contains six polysaccharide deacetylase gene
homologs: pdaA, pdaB (previously known as ybaN), yheN,
yjeA, yxkH and ylxY. This family is represented by
Bacillus subtilis putative polysaccharide deacetylase
BsYlxY, encoded by the ylxY gene, which is a member of
the carbohydrate esterase 4 (CE4) superfamily. Although
its biological function still remains unknown, BsYlxY
shows high sequence homology to the catalytic domain of
Bacillus subtilis pdaB gene encoding a putative
polysaccharide deacetylase (BsPdaB), which is essential
for the maintenance of spores after the late stage of
sporulation and is highly conserved in spore-forming
bacteria. However, disruption of the ylxY gene in B.
subtilis did not cause any sporulation defect. Moreover,
the Asp residue in the classical His-His-Asp
zinc-binding motif of CE4 esterases is mutated to a Val
residue in this family. Other catalytically relevant
residues of CE4 esterases are also not conserved, which
suggest that members of this family may be inactive.
Length = 188
Score = 41.5 bits (98), Expect = 3e-04
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 212 DIKATFFVSHKYT--NYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMR 269
D+KATFF+ ++ N V+++ + GHE+ H +H D ++ K
Sbjct: 32 DVKATFFLEGRWAKKNPDLVRKIAKDGHEIGNHGYSHPDPSQLSYEQNREEIRK---TNE 88
Query: 270 IIAE 273
II E
Sbjct: 89 IIEE 92
>gnl|CDD|213023 cd10918, CE4_NodB_like_5s_6s, Putative catalytic NodB homology
domain of PgaB, IcaB, and similar proteins which consist
of a deformed (beta/alpha)8 barrel fold with 5- or
6-strands. This family belongs to the large and
functionally diverse carbohydrate esterase 4 (CE4)
superfamily, whose members show strong sequence
similarity with some variability due to their distinct
carbohydrate substrates. It includes bacterial
poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB,
hemin storage system HmsF protein in gram-negative
species, intercellular adhesion proteins IcaB, and many
uncharacterized prokaryotic polysaccharide deacetylases.
It also includes a putative polysaccharide deacetylase
YxkH encoded by the Bacillus subtilis yxkH gene, which
is one of six polysaccharide deacetylase gene homologs
present in the Bacillus subtilis genome. Sequence
comparison shows all family members contain a conserved
domain similar to the catalytic NodB homology domain of
rhizobial NodB-like proteins, which consists of a
deformed (beta/alpha)8 barrel fold with 6 or 7 strands.
However, in this family, most proteins have 5 strands
and some have 6 strands. Moreover, long insertions are
found in many family members, whose function remains
unknown.
Length = 157
Score = 40.7 bits (96), Expect = 4e-04
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 29/104 (27%)
Query: 183 ITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVS-----------------HKYTN 225
+TFDD +N + K+ + ATFFV Y
Sbjct: 4 LTFDDGYRDNYTYALPIL---KKYG-----LPATFFVITGYIGGGNPWWAPAPPRPPYLT 55
Query: 226 YSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMR 269
+ ++EL G E+ H+ TH D + + ++ +E+A +
Sbjct: 56 WDQLRELAASGVEIGSHTHTHPD----LTTLSDEELRRELAESK 95
>gnl|CDD|200572 cd10948, CE4_BsPdaA_like, Catalytic NodB homology domain of
Bacillus subtilis polysaccharide deacetylase PdaA, and
its bacterial homologs. The Bacillus subtilis genome
contains six polysaccharide deacetylase gene homologs:
pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH
and ylxY. This family is represented by Bacillus
subtilis pdaA gene encoding polysaccharide deacetylase
BsPdaA, which is a member of the carbohydrate esterase 4
(CE4) superfamily. BsPdaA deacetylates peptidoglycan
N-acetylmuramic acid (MurNAc) residues to facilitate the
formation of muramic delta-lactam, which is required for
recognition of germination lytic enzymes. BsPdaA
deficiency leads to the absence of muramic delta-lactam
residues in the spore cortex. Like other CE4 esterases,
BsPdaA consists of a single catalytic NodB homology
domain that appears to adopt a deformed (beta/alpha)8
barrel fold with a putative substrate binding groove
harboring the majority of the conserved residues. It
utilizes a general acid/base catalytic mechanism
involving a tetrahedral transition intermediate, where a
water molecule functions as the nucleophile tightly
associated to the zinc cofactor.
Length = 223
Score = 41.1 bits (97), Expect = 5e-04
Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 16/111 (14%)
Query: 140 ENDPNRAPPCDPAVCVLPDCFCSEDGTYIPGDLPSKEVPQMITITFDDAINNNNIALYKE 199
N PP A L + + Y G+ K I +TFD+ N +
Sbjct: 8 SKSKNHQPP---ATGKLYNELIKKYNAYYVGNSKEKV----IYLTFDEGYENGYT---PK 57
Query: 200 MFNGKRKNPNGCDIKATFFVSHKY--TNYSAVQELHRKGHEVAVHSITHND 248
+ + +KN D+KATFFV+ Y +N ++ + +GH + H++ H D
Sbjct: 58 ILDVLKKN----DVKATFFVTGHYVKSNPDLIKRMVDEGHIIGNHTVHHPD 104
>gnl|CDD|200571 cd10947, CE4_SpPgdA_BsYjeA_like, Catalytic NodB homology domain of
Streptococcus pneumoniae peptidoglycan deacetylase PgdA,
Bacillus subtilis BsYjeA protein, and their bacterial
homologs. This family is represented by Streptococcus
pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA), a
member of the carbohydrate esterase 4 (CE4) superfamily.
SpPgdA protects gram-positive bacterial cell wall from
host lysozymes by deacetylating peptidoglycan
N-acetylglucosamine (GlcNAc) residues. It consists of
three separate domains: N-terminal, middle and
C-terminal (catalytic) domains. The catalytic NodB
homology domain is similar to the deformed (beta/alpha)8
barrel fold adopted by other CE4 esterases, which
harbors a mononuclear metalloenzyme employing a
conserved His-His-Asp zinc-binding triad closely
associated with conserved catalytic base (aspartic acid)
and acid (histidine) to carry out acid/base catalysis.
The enzyme is able to accept GlcNAc3 as a substrate,
with the N-acetyl of the middle sugar being removed by
the enzyme. This family also includes Bacillus subtilis
BsYjeA protein encoded by the yjeA gene, which is one of
the six polysaccharide deacetylase gene homologs (pdaA,
pdaB/ybaN, yheN, yjeA, yxkH and ylxY) in the Bacillus
subtilis genome. Although homology comparison shows that
the BsYjeA protein contains a polysaccharide deacetylase
domain, and was predicted to be a membrane-bound
xylanase or a membrane-bound chitooligosaccharide
deacetylase, more recent research indicates BsYjeA might
be a novel non-specific secretory endonuclease which
creates random nicks progressively on the two strands of
dsDNA, resulting in highly distinguishable
intermediates/products very different in chemical and
physical compositions over time. In addition, BsYjeA
shares several enzymatic properties with the
well-understood DNase I endonuclease. Both enzymes are
active on ssDNA and dsDNA, both generate random nicks,
and both require Mg2+ or Mn2+ for hydrolytic activity.
Length = 177
Score = 40.1 bits (94), Expect = 7e-04
Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 24/116 (20%)
Query: 181 ITITFDD----AINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYTNYSAVQELHR 234
+ +TFDD + K K K ATFF+ S+ T V+ +
Sbjct: 3 VALTFDDGPDPTTTPQVLKTLK-----KYK------APATFFMLGSNVKTYPELVRRVLD 51
Query: 235 KGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPY 290
GHE+ HS +H + +V + K++ EK + N +R PY
Sbjct: 52 AGHEIGNHSWSHPQ----LTKLSVAEAEKQINDTDDAIEK---ATGNRPTLLRPPY 100
>gnl|CDD|200576 cd10952, CE4_MrCDA_like, Catalytic NodB homology domain of Mucor
rouxii chitin deacetylase and similar proteins. This
family is represented by the chitin deacetylase (MrCDA,
EC 3.5.1.41) encoded from the fungus Mucor rouxii (also
known as Amylomyces rouxii). MrCDA is an acidic
glycoprotein with a very stringent specificity for
beta1-4-linked N-acetylglucosamine homopolymers. It
requires at least four residues (chitotetraose) for
catalysis, and can achieve extensive deacetylation on
chitin polymers. MrCDA shows high sequence similarity to
Colletotrichum lindemuthianum chitin deacetylase
(endo-chitin de-N-acetylase, ClCDA), which consists of a
single catalytic domain similar to the deformed
(beta/alpha)8 barrel fold adopted by the carbohydrate
esterase 4 (CE4) superfamily, which encompasses a
mononuclear metalloenzyme employing a conserved
His-His-Asp zinc-binding triad closely associated with
the conserved catalytic base (aspartic acid) and acid
(histidine) to carry out acid/base catalysis. The family
also includes some uncharacterized eukaryotic and
bacterial homologs of MrCDA.
Length = 178
Score = 40.0 bits (94), Expect = 8e-04
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 183 ITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYTNYSAVQELHRKGHEVA 240
+TFDD AL + K N KATFFV S+ N +Q GHE+
Sbjct: 5 LTFDDGPTPATPALLDYL---KSHN-----QKATFFVIGSNVVNNPDILQRALEAGHEIG 56
Query: 241 VHSITH 246
VH+ +H
Sbjct: 57 VHTWSH 62
>gnl|CDD|200582 cd10959, CE4_NodB_like_3, Catalytic NodB homology domain of
uncharacterized bacterial polysaccharide deacetylases.
This family includes many uncharacterized bacterial
polysaccharide deacetylases. Although their biological
function still remains unknown, members in this family
show high sequence homology to the catalytic NodB
homology domain of Streptococcus pneumoniae
polysaccharide deacetylase PgdA (SpPgdA), which is an
extracellular metal-dependent polysaccharide deacetylase
with de-N-acetylase activity toward a hexamer of
chitooligosaccharide N-acetylglucosamine, but not
shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. Like SpPgdA, this family
is a member of the carbohydrate esterase 4 (CE4)
superfamily.
Length = 187
Score = 39.9 bits (94), Expect = 9e-04
Identities = 22/95 (23%), Positives = 36/95 (37%), Gaps = 14/95 (14%)
Query: 211 CDIKATFFV-SHKYTNYSA-VQELHRKGHEVAVHSITHNDDENFWS-NATVDDWAKEMAG 267
KATFFV + + ++ + +GHE+ H H S + D +
Sbjct: 26 HGAKATFFVVGERAERHPDLIRRIVDEGHEIGNHGYRHRHP-WLRSPWKAIRDLRR---A 81
Query: 268 MRIIAEKYANLSDNSVVGVRAPYLRVGGNNQFTMM 302
RII + L+ R P+ G N T++
Sbjct: 82 ARIIEQ----LTGRPPRYYRPPW---GHLNLATLL 109
>gnl|CDD|200580 cd10956, CE4_BH1302_like, Putative catalytic NodB homology domain
of uncharacterized BH1302 protein from Bacillus
halodurans and its bacterial homologs. This family is
represented by a putative polysaccharide deacetylase
BH1302 from Bacillus halodurans. Although its biological
function is unknown, BH1302 shows high sequence homology
to the catalytic NodB homology domain of Streptococcus
pneumoniae polysaccharide deacetylase PgdA (SpPgdA),
which is an extracellular metal-dependent polysaccharide
deacetylase with de-N-acetylase activity toward a
hexamer of chitooligosaccharide N-acetylglucosamine, but
not shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. Both BH1302 and SpPgdA
belong to the carbohydrate esterase 4 (CE4) superfamily.
This family also includes many uncharacterized bacterial
polysaccharide deacetylases.
Length = 194
Score = 39.2 bits (92), Expect = 0.002
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 9/69 (13%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKYT--NYSAVQELHRKGHE 238
I +TFDD + + + DIKATFF+ + N S + + GHE
Sbjct: 7 IALTFDDGPTPAHTDAILSILDEY-------DIKATFFLIGREIEENPSEARAIVAAGHE 59
Query: 239 VAVHSITHN 247
+ HS +H
Sbjct: 60 IGNHSYSHR 68
>gnl|CDD|200600 cd10978, CE4_Sll1306_like, Putative catalytic domain of
Synechocystis sp. Sll1306 protein and other bacterial
homologs. The family contains Synechocystis sp. Sll1306
protein and uncharacterized bacterial polysaccharide
deacetylases. Although their biological function remains
unknown, they show very high sequence homology to the
catalytic domain of bacterial PuuE (purine utilization
E) allantoinases. PuuE allantoinase specifically
catalyzes the hydrolysis of (S)-allantoin into allantoic
acid. It functions as a homotetramer. Its monomer is
composed of a 7-stranded barrel with detectable sequence
similarity to the 6-stranded barrel NodB homology domain
of polysaccharide deacetylase-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. PuuE allantoinase
appears to be metal-independent and acts on a small
substrate molecule, which is distinct from the common
feature of polysaccharide deacetylases that are normally
metal ion dependent and recognize multimeric substrates.
Length = 271
Score = 37.0 bits (86), Expect = 0.013
Identities = 25/108 (23%), Positives = 43/108 (39%), Gaps = 17/108 (15%)
Query: 230 QELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKYANLSDNSVVGVRAP 289
+E+ ++GHE A H W N +E A ++ + ++ VG A
Sbjct: 86 KEIVQRGHEAAAHGRD-------WQNQFSMSREQERAFIQDGVDSIQKVTGQRPVGYNAF 138
Query: 290 YLRVGGNNQFTMMEEQAFLY-------DSTITAPLSNPPLW--PYTMY 328
+LR G N +++E F+Y D P++ PYT+
Sbjct: 139 WLR-GSPNTLDILQELGFVYHIDDVSRDEPFIIPVNGKDFVVVPYTLR 185
>gnl|CDD|200584 cd10962, CE4_GT2-like, Catalytic NodB homology domain of
uncharacterized bacterial glycosyl transferase, group
2-like family proteins. This family includes many
uncharacterized bacterial proteins containing an
N-terminal GH18 (glycosyl hydrolase, family 18) domain,
a middle NodB-like homology domain, and a C-terminal
GT2-like (glycosyl transferase group 2) domain. Although
their biological function is unknown, members in this
family contain a middle NodB homology domain that is
similar to the catalytic domain of Streptococcus
pneumoniae polysaccharide deacetylase PgdA (SpPgdA), an
extracellular metal-dependent polysaccharide deacetylase
with de-N-acetylase activity toward a hexamer of
chitooligosaccharide N-acetylglucosamine, but not
shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. Like SpPgdA, this family
is a member of the carbohydrate esterase 4 (CE4)
superfamily. The presence of three domains suggests that
members of this family may be multifunctional.
Length = 196
Score = 33.8 bits (78), Expect = 0.095
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 212 DIKATFFV--SHKYTNYSAVQELHRKGHEVAVHSITHND 248
I ATFFV + N V+ + +GHE+ H+ TH D
Sbjct: 27 QIPATFFVIGENAVNNPELVKRIIDEGHEIGNHTFTHPD 65
>gnl|CDD|200581 cd10958, CE4_NodB_like_2, Catalytic NodB homology domain of
uncharacterized chitin deacetylases and hypothetical
proteins. This family includes some uncharacterized
chitin deacetylases and hypothetical proteins, mainly
from eukaryotes. Although their biological function is
unknown, members in this family show high sequence
homology to the catalytic NodB homology domain of
Colletotrichum lindemuthianum chitin deacetylase
(endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41), which
catalyzes the hydrolysis of N-acetamido groups of
N-acetyl-D-glucosamine residues in chitin, converting it
to chitosan in fungal cell walls. Like ClCDA, this
family is a member the carbohydrate esterase 4 (CE4)
superfamily.
Length = 190
Score = 33.4 bits (77), Expect = 0.13
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 179 QMITITFDDA---INNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYTNYSAVQELH 233
+++ +T DDA + L +E +++ATFFV SH + +
Sbjct: 1 KVVALTIDDAPSPSTEEILDLLEEH-----------NVRATFFVIGSHAPRREEVLSRIV 49
Query: 234 RKGHEVAVH 242
+GHE+ H
Sbjct: 50 EEGHELGNH 58
>gnl|CDD|213027 cd10970, CE4_DAC_u1_6s, Putative catalytic NodB homology domain of
uncharacterized prokaryotic polysaccharide deacetylases
which consist of a 6-stranded beta/alpha barrel. This
family contains uncharacterized prokaryotic
polysaccharide deacetylases. Although their biological
functions remain unknown, all members of the family
contain a conserved domain with a 6-stranded beta/alpha
barrel, which is similar to the catalytic NodB homology
domain of rhizobial NodB-like proteins, belonging to the
larger carbohydrate esterase 4 (CE4) superfamily.
Length = 194
Score = 33.4 bits (77), Expect = 0.16
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 18/75 (24%)
Query: 180 MITITFDDAINNNNIALYKEMFNGKRKNP--NGCDIKATFFV------SHKYTNYSAVQE 231
+++TFDD + Y F P I AT V S ++E
Sbjct: 2 KVSLTFDD----GYESQYTTAF------PILQEYGIPATAAVIPDSIGSSGRLTLDQLRE 51
Query: 232 LHRKGHEVAVHSITH 246
L G E+A H++TH
Sbjct: 52 LQDAGWEIASHTLTH 66
>gnl|CDD|200570 cd10946, CE4_Mll8295_like, Putative catalytic NodB homology domain
of uncharacterized Mll8295 protein encoded from
Rhizobium loti and its bacterial homologs. This family
is represented by a putative polysaccharide deacetylase
Mll8295 encoded from Rhizobium loti. Although its
biological function still remains unknown, Mll8295 shows
high sequence homology to the catalytic domain of
Streptococcus pneumoniae polysaccharide deacetylase PgdA
(SpPgdA), which is an extracellular metal-dependent
polysaccharide deacetylase with de-N-acetylase activity
toward a hexamer of chitooligosaccharide
N-acetylglucosamine, but not shorter
chitooligosaccharides or a synthetic peptidoglycan
tetrasaccharide. Both Mll8295 and SpPgdA belong to the
carbohydrate esterase 4 (CE4) superfamily. This family
also includes many uncharacterized bacterial
polysaccharide deacetylases.
Length = 217
Score = 33.1 bits (76), Expect = 0.22
Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 16/86 (18%)
Query: 179 QMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFV--SHKYT---NYSAVQE-L 232
+ I +TFDD + + K + +KAT F+ H A++ L
Sbjct: 1 KTIYLTFDDGPLDGTENILKILKAEN--------VKATVFLVGFHADGGDKAKEALKLYL 52
Query: 233 HRKGHEVAVHSITH--NDDENFWSNA 256
G +A HS TH N+ F+SN
Sbjct: 53 DNPGIILANHSYTHANNNYTLFYSNT 78
>gnl|CDD|200557 cd10931, CE4_u7, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 224
Score = 32.6 bits (75), Expect = 0.36
Identities = 26/117 (22%), Positives = 44/117 (37%), Gaps = 32/117 (27%)
Query: 212 DIKATFFV------SHKYTNYSA--------VQELHRKGHEVAVHSITHNDDENFWSNAT 257
+++TFF + NYS ++E+ +G E+ +H ++ S
Sbjct: 27 GVRSTFFFLAGDYSPYDDGNYSYNDPKIRSLIKEIADRGWEIGLHG-------SYNSYTD 79
Query: 258 VDDWAKEMAGMRIIAEKYANLSDNSVVGVRAPYLRVGGNNQFTM--MEEQAFLYDST 312
+ KE E+ + V G R YLR + T + + F YDST
Sbjct: 80 PEKLKKEK-------ERLEKILGRPVTGGRQHYLRF--DLPETWRNLADAGFTYDST 127
>gnl|CDD|200577 cd10953, CE4_SlAXE_like, Catalytic NodB homology domain of
Streptomyces lividans acetylxylan esterase and its
bacterial homologs. This family is represented by
Streptomyces lividans acetylxylan esterase (SlAXE, EC
3.1.1.72), a member of the carbohydrate esterase 4 (CE4)
superfamily. SlAXE deacetylates O-acetylated xylan, a
key component of plant cell walls. It shows no
detectable activity on generic esterase substrates
including para-nitrophenyl acetate. It is specific for
sugar-based substrates and will precipitate acetylxylan
as a result of deacetylation. SlAXE also functions as a
chitin and chitooligosaccharide de-N-acetylase with
equal efficiency to its activity on xylan. SlAXE forms a
dimer. Each monomer contains a catalytic NodB homology
domain with the same overall topology and a deformed
(beta/alpha)8 barrel fold as other CE4 esterases, which
encompasses a mononuclear metalloenzyme employing a
conserved His-His-Asp zinc-binding triad closely
associated with the conserved catalytic base (aspartic
acid) and acid (histidine), to carry out acid/base
catalysis. SlAXE possess a single metal center with a
chemical preference for Co2+.
Length = 179
Score = 31.8 bits (72), Expect = 0.42
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKY--TNYSAVQELHRKGHE 238
+ +TFDD NN+N A + + ++N ++AT F + +N S ++ G
Sbjct: 3 VGLTFDDGPNNSNTA---TLLSALKQN----GLRATLFNQGQNAQSNPSLMRAQKNAGMW 55
Query: 239 VAVHSITHNDDENFWSNATVDD 260
+ HS +H + WS +
Sbjct: 56 IGNHSWSHPHMTS-WSYQQMYS 76
>gnl|CDD|131920 TIGR02873, spore_ylxY, probable sporulation protein, polysaccharide
deacetylase family. Members of this protein family are
most closely related to TIGR02764, a subset of
polysaccharide deacetylase family proteins found in a
species if and only if the species forms endospores like
those of Bacillus subtilis or Clostridium tetani. This
family is likewise restricted to spore-formers, but is
not universal among them in having sequences with
full-length matches to the model [Energy metabolism,
Biosynthesis and degradation of polysaccharides,
Cellular processes, Sporulation and germination].
Length = 268
Score = 32.5 bits (74), Expect = 0.43
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 212 DIKATFFVSHKYT--NYSAVQELHRKGHEVAVHSITHND 248
D+KATFF+ K+ N + + +GHE+ H+ H D
Sbjct: 111 DVKATFFLEGKWVKENSQLAKMIVEQGHEIGNHAYNHPD 149
>gnl|CDD|200565 cd10940, CE4_PuuE_HpPgdA_like_1, Putative catalytic domain of
uncharacterized bacterial polysaccharide deacetylases
similar to bacterial PuuE allantoinases and Helicobacter
pylori peptidoglycan deacetylase (HpPgdA). This family
contains many uncharacterized bacterial polysaccharide
deacetylases (DCAs) that show high sequence similarity
to the catalytic domain of bacterial PuuE allantoinases
and Helicobacter pylori peptidoglycan deacetylase
(HpPgdA). PuuE allantoinase appears to be
metal-independent and specifically catalyzes the
hydrolysis of (S)-allantoin into allantoic acid.
Different from PuuE allantoinase, HpPgdA has the ability
to bind a metal ion at the active site and is
responsible for a peptidoglycan modification that
counteracts the host immune response. Both PuuE
allantoinase and HpPgdA function as homotetramers. The
monomer is composed of a 7-stranded barrel with
detectable sequence similarity to the 6-stranded barrel
NodB homology domain of DCA-like proteins in the CE4
superfamily, which removes N-linked or O-linked acetyl
groups from cell wall polysaccharides. In contrast to
typical NodB-like DCAs, PuuE allantoinase and HpPgdA do
not exhibit a solvent-accessible polysaccharide binding
groove and might only bind a small molecule at the
active site.
Length = 306
Score = 32.0 bits (73), Expect = 0.65
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 212 DIKATFFV-----SHKYTNYSAVQELHRKGHEVAVHSITH 246
+ T FV + N A++ + GHE+A HS H
Sbjct: 45 GLTITVFVVGRDLARD-ENAKALRAIADAGHEIANHSFAH 83
>gnl|CDD|200568 cd10943, CE4_NodB, Putative catalytic domain of rhizobial NodB
chitooligosaccharide N-deacetylase and its bacterial
homologs. This family corresponds to rhizobial NodB
chitooligosaccharide N-deacetylase (EC 3.5.1.-), encoded
by nodB gene from the nodulation (nod) gene cluster that
is responsible for the biosynthesis of bacterial
nodulation signals, termed Nod factors. NodB is involved
in de-N-acetylating the nonreducing N-acetylglucosamine
residue of chitooligosaccharides to allow for the
attachment of the fatty acyl group by the
acyltransferase NodA. The monosaccharide
N-acetylglucosamine cannot be deacetylated by NodB. NodB
is composed of a 6-stranded barrel catalytic domain with
detectable sequence similarity to the 7-stranded barrel
homology domain of polysaccharide deacetylase (DCA)-like
proteins in the larger carbohydrate esterase 4 (CE4)
superfamily.
Length = 193
Score = 30.2 bits (68), Expect = 1.5
Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 21/76 (27%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDI------KATFFVSHKYT--NYSAVQEL 232
I +TFDD N P D+ ATFFV Y + ++ +
Sbjct: 3 IYLTFDDGPN-------------PSCTPQVLDVLAEHRVPATFFVIGAYAAEHPELIRRM 49
Query: 233 HRKGHEVAVHSITHND 248
+GHEV H++TH D
Sbjct: 50 IAEGHEVGNHTMTHPD 65
>gnl|CDD|211966 TIGR04243, nodulat_NodB, chitooligosaccharide deacetylase NodB.
Nodulation factors are lipooligosaccharide signalling
molecules produced by rhizobia, the symbiotic
nitrogen-fixing bacteria that form nodules in plants.
These Nod factor sustems have the NodABC genes in common
but differ subtly in what they produce, which affects
host range. NodB is a chitooligosaccharide deacetylase.
Length = 197
Score = 30.5 bits (69), Expect = 1.6
Identities = 25/78 (32%), Positives = 32/78 (41%), Gaps = 25/78 (32%)
Query: 181 ITITFDDAINNNNIALYKEMFNGKRKNPNGCDI------KATFFVSHKYTNYSAVQELHR 234
+ +TFDD N P D+ ATFFV Y + EL R
Sbjct: 4 VYLTFDDGPN-------------PFCTPQILDVLAEHRVPATFFVIGAYA--AEHPELIR 48
Query: 235 K----GHEVAVHSITHND 248
+ GHEVA H++TH D
Sbjct: 49 RIIAEGHEVANHTMTHPD 66
>gnl|CDD|200594 cd10972, CE4_DAC_u3_5s, Putative catalytic NodB homology domain of
uncharacterized bacterial polysaccharide deacetylases
which consist of a 5-stranded beta/alpha barrel. This
family contains uncharacterized bacterial polysaccharide
deacetylases. Although their biological functions remain
unknown, all members of the family are predicted to
contain a conserved domain with a 5-stranded beta/alpha
barrel, which is similar to the catalytic NodB homology
domain of rhizobial NodB-like proteins, belonging to the
larger carbohydrate esterase 4 (CE4) superfamily.
Length = 216
Score = 30.4 bits (69), Expect = 1.7
Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 23/87 (26%)
Query: 181 ITITFDDAINNNNIALYKEMFNG--------------KRKNPNGCDIKATFFV------- 219
+ +TFDD + ++ K ++P TF+V
Sbjct: 7 VVLTFDDG-SPGQFRYIEKNGQLVIDPDTAVGILEDFKEEHP-DFPPTGTFYVNPGPFGF 64
Query: 220 SHKYTNYSAVQELHRKGHEVAVHSITH 246
++ L G+E+ H+ TH
Sbjct: 65 GQPEYAEQKLRWLVELGYEIGNHTYTH 91
>gnl|CDD|200558 cd10932, CE4_u8, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 324
Score = 30.4 bits (69), Expect = 2.2
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 19/51 (37%)
Query: 211 CDIKATFFVS----HKYTNYSA---------------VQELHRKGHEVAVH 242
+K TFFV K S ++EL +GH++ +H
Sbjct: 38 VGVKLTFFVDVGMLEKLKELSERFPKTEYDYNAIKNQLRELVAQGHDIQLH 88
>gnl|CDD|200567 cd10942, CE4_u11, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 252
Score = 30.1 bits (68), Expect = 2.4
Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 15/107 (14%)
Query: 209 NGCDIKATFFV-SHKYTNY-SAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMA 266
+ I+ T+FV +Y ++ + GHE+ +H H W+ + +
Sbjct: 44 DELGIRCTYFVEGWSALHYPDELEAILAHGHEIGLHGWQHEP----WAGLS------PLE 93
Query: 267 GMRIIAEKYANLSDNSV--VGVRAPYLRVGGNNQFTMMEEQAFLYDS 311
+I + + VG R P +G + + + Y S
Sbjct: 94 EDDLINRSLSIAERLGLAPVGFRPPGGALGAHTLALLAKH-GIRYVS 139
>gnl|CDD|131930 TIGR02884, spore_pdaA, delta-lactam-biosynthetic de-N-acetylase.
Muramic delta-lactam is an unusual constituent of
peptidoglycan, found only in bacterial spores in the
peptidoglycan wall, or spore cortex. The proteins in
this family are PdaA (yfjS), a member of a larger family
of polysaccharide deacetylases, and are specificially
involved in delta-lactam biosynthesis. PdaA acts
immediately after CwlD, an N-acetylmuramoyl-L-alanine
amidase and performs a de-N-acetylation. PdaA may also
perform the following transpeptidation for lactam ring
formation, as heterologous expression in E. coli of CwlD
and PdaA together is sufficient for delta-lactam
production [Cell envelope, Biosynthesis and degradation
of murein sacculus and peptidoglycan, Cellular
processes, Sporulation and germination].
Length = 224
Score = 29.7 bits (67), Expect = 2.7
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 14/87 (16%)
Query: 164 DGTYIPGDLPSKEVPQMITITFDDAINNNNIALYKEMFNGKRKNPNGCDIKATFFVSHKY 223
+ Y+ GD K I +TFD+ N ++ + ++ + A FFV+ Y
Sbjct: 27 NAYYL-GDTSKKV----IYLTFDNGYENGYTP---KILDVLKEK----KVPAAFFVTGHY 74
Query: 224 --TNYSAVQELHRKGHEVAVHSITHND 248
T ++ + +GH V HS+ H
Sbjct: 75 IKTQPDLIKRMVDEGHIVGNHSVHHPS 101
>gnl|CDD|226186 COG3660, COG3660, Predicted nucleoside-diphosphate-sugar epimerase
[Cell envelope biogenesis, outer membrane].
Length = 329
Score = 29.8 bits (67), Expect = 3.2
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 293 VGGNN-QFTMMEEQAFLYDSTITAPLSNPPLWPYTMYF--RMPHRCHGNLQ-HCPTRSHA 348
VGGNN F E++A + S + L N + + F R P L+ + +
Sbjct: 168 VGGNNKAFVFQEDKAHQFASLLVKILENQG-GSFLISFSRRTPDTVKSILKNNLNSSPGI 226
Query: 349 VWEMVMNELDRREDPNFD 366
VW N D +P D
Sbjct: 227 VW----NNEDTGYNPYID 240
>gnl|CDD|200559 cd10933, CE4_u9, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 266
Score = 29.6 bits (67), Expect = 3.2
Identities = 31/187 (16%), Positives = 54/187 (28%), Gaps = 35/187 (18%)
Query: 209 NGCDIKATFFV----SHKYTNYSA-----VQELHRKGHEVAVHSITHNDDENFWSNATVD 259
N +K TFFV + ++ V+ + +GH+V +H DE D
Sbjct: 49 NRYGLKGTFFVEPLPALRF--GDEPLEDIVRLIVARGHDVQLHLHPEWLDEARPLLPGGD 106
Query: 260 DWAKEMAGM------RIIAEKYANLSDNSVVGVRAPYLRVGG----NNQFTMMEEQAFLY 309
+ M ++I E L A R GG ++ +
Sbjct: 107 RNRRHMHDYSLEEQTQLIEEGRDLLKRAGAPDPIA--FRAGGFGANDDTLRALAANGIRI 164
Query: 310 DSTITAPLSNPPLWPYTMYFRMPHRCHGNLQHCPTRSHAVWEMVMNELDRREDPNFDEYL 369
DS+ P + +G P + V E+ + P +
Sbjct: 165 DSSYNYCYLGPG-----CNISLERTLNG-----PVKIEGVLEVPVTVFKDG--PGRLRHA 212
Query: 370 PGCAMVD 376
A+
Sbjct: 213 QVTALSL 219
>gnl|CDD|147504 pfam05352, Phage_connector, Phage Connector (GP10). The head-tail
connector of bacteriophage 29 is composed of 12 36 kDa
subunits with 12 fold symmetry. It is the central
component of a rotary motor that packages the genomic
dsDNA into pre-formed proheads. This motor consists of
the head-tail connector, surrounded by a 29-encoded,
174-base, RNA and a viral ATPase protein.
Length = 281
Score = 29.1 bits (65), Expect = 4.6
Identities = 16/87 (18%), Positives = 36/87 (41%), Gaps = 12/87 (13%)
Query: 216 TFFVSHKYTNYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMRIIAEKY 275
+ K NY +++L K + + +N+D + ++ +A+++A ++ +
Sbjct: 92 NYQKQFKLYNYRVIEDLKEKNMGIVI----YNNDFYEPTLPYLELFAEKLAELKETIQVN 147
Query: 276 ANLSDNSVVGVRAPYL-RVGGNNQFTM 301
N + P L NNQ +M
Sbjct: 148 QNAQ-------KTPVLIFANDNNQLSM 167
>gnl|CDD|200599 cd10977, CE4_PuuE_SpCDA1, Catalytic domain of bacterial PuuE
allantoinases, Schizosaccharomyces pombe chitin
deacetylase 1 (SpCDA1), and similar proteins.
Allantoinase (EC 3.5.2.5) can hydrolyze
allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the
most important nitrogen carrier for some plants, soil
animals, and microorganisms, to allantoate. DAL1 gene
from Saccharomyces cerevisiae encodes an allantoinase.
However, some organisms possess allantoinase activity
but lack DAL1 allantoinase. In those organisms, a
defective allantoinase gene, named puuE (purine
utilization E), encodes an allantoinase that
specifically catalyzes the hydrolysis of (S)-allantoin
into allantoic acid. PuuE allantoinase is related to
polysaccharide deacetylase (DCA), one member of the
carbohydrate esterase 4 (CE4) superfamily, that removes
N-linked or O-linked acetyl groups of cell wall
polysaccharides, and lacks sequence similarity with the
known DAL1 allantoinase that belongs to the
amidohydrolase superfamily. PuuE allantoinase functions
as a homotetramer. Its monomer is composed of a
7-stranded barrel with detectable sequence similarity to
the 6-stranded barrel NodB homology domain of DCAs. It
appears to be metal-independent and acts on a small
substrate molecule, which is distinct from the common
features of DCAs that are normally metal ion dependent
and recognize multimeric substrates. This family also
includes a chitin deacetylase 1 (SpCDA1) encoded by the
Schizosaccharomyces pombe cda1 gene. Although the
general function of chitin deacetylase (CDA) is the
synthesis of chitosan from chitin, a polymer of N-acetyl
glucosamine, to build up the proper ascospore wall, the
actual function of SpCDA1 might involve allantoin
hydrolysis. It is likely orthologous to PuuE
allantoinase, whereas it is more distantly related to
the CDAs found in other fungi, such as Saccharomyces
cerevisiae and Mucor rouxii. Those CDAs are similar with
rizobial NodB protein and are not included in this
family.
Length = 273
Score = 28.8 bits (65), Expect = 6.1
Identities = 26/105 (24%), Positives = 39/105 (37%), Gaps = 17/105 (16%)
Query: 212 DIKATFFVSHKYT--NYSAVQELHRKGHEVAVHSITHNDDENFWSNATVDDWAKEMAGMR 269
D+ T F N + + + GHE+A H D + D A+E +R
Sbjct: 73 DVPLTVFAVAMALERNPAVARAMVAAGHEIASHGWRWIDYQGM-------DEAEEREHIR 125
Query: 270 IIAEKYANLSDNSVVGV---RAPYLRVGGNNQFTMMEEQAFLYDS 311
L+ +G RA N + ++EE FLYDS
Sbjct: 126 RAIAIIERLTGERPLGWYTGRAS-----PNTRRLVVEEGGFLYDS 165
>gnl|CDD|213028 cd10973, CE4_DAC_u4_5s, Putative catalytic NodB homology domain of
uncharacterized bacterial polysaccharide deacetylases
which consist of a 5-stranded beta/alpha barrel. This
family contains many uncharacterized bacterial
polysaccharide deacetylases. Although their biological
functions remain unknown, all members of the family are
predicted to contain a conserved domain with a
5-stranded beta/alpha barrel, which is similar to the
catalytic NodB homology domain of rhizobial NodB-like
proteins, belonging to the larger carbohydrate esterase
4 (CE4) superfamily.
Length = 157
Score = 28.0 bits (63), Expect = 7.0
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 22/79 (27%)
Query: 181 ITITFDDAINNNNIALYKE---MFNGKRKNPNGCDIKATFFV-----SHKYTNY---SAV 229
+ IT DD + Y + K P T FV Y +Y +
Sbjct: 3 VVITIDDGYKSV----YTNAFPILK-KYGYP------FTLFVYTEAIGRGYPDYLSWDQI 51
Query: 230 QELHRKGHEVAVHSITHND 248
+E+ + G E+A HS +H
Sbjct: 52 REMAKYGVEIANHSYSHPH 70
>gnl|CDD|132187 TIGR03143, AhpF_homolog, putative alkyl hydroperoxide reductase F
subunit. This family of thioredoxin reductase homologs
is found adjacent to alkylhydroperoxide reductase C
subunit predominantly in cases where there is only one C
subunit in the genome and that genome is lacking the F
subunit partner (also a thioredcxin reductase homolog)
that is usually found (TIGR03140).
Length = 555
Score = 29.0 bits (65), Expect = 7.0
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 164 DGTYIPGDLPSKEVPQMITITFDDAI 189
G Y GDL KE+ Q++T D AI
Sbjct: 274 PGVYAAGDLRPKELRQVVTAVADGAI 299
>gnl|CDD|193222 pfam12746, GNAT_acetyltran, GNAT acetyltransferase. Many of the
members are annotated s being Zwittermicin A resistance
proteins, whereas others are listed as being GNAT
acetyltransferases. The family has similarities to the
GNAT acetyltransferase family.
Length = 269
Score = 28.5 bits (63), Expect = 7.1
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 249 DENFWSNATVDDWAKEMAGMRIIAEKYANL 278
DEN +++ +K+ G I E + +L
Sbjct: 139 DENIVEACLLEEVSKDFTGNFIDVEDFIDL 168
>gnl|CDD|176908 cd08899, SRPBCC_CalC_Aha1-like_6, Putative hydrophobic
ligand-binding SRPBCC domain of an uncharacterized
subgroup of CalC- and Aha1-like proteins. SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a
functionally uncharacterized subgroup of CalC- and
Aha1-like proteins. This group shows similarity to the
SRPBCC domains of Micromonospora echinospora CalC (a
protein which confers resistance to enediynes) and human
Aha1 (one of several co-chaperones which regulate the
dimeric chaperone Hsp90), and belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
Length = 157
Score = 27.6 bits (62), Expect = 9.3
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 291 LRVGGNNQFTMMEEQAFLYDSTITA 315
LRVGG +F M +E+ TI A
Sbjct: 47 LRVGGRVEFVMDDEEGPNATGTILA 71
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
0.320 0.136 0.442
Gapped
Lambda K H
0.267 0.0665 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,389,477
Number of extensions: 2331229
Number of successful extensions: 1853
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1805
Number of HSP's successfully gapped: 61
Length of query: 476
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 375
Effective length of database: 6,457,848
Effective search space: 2421693000
Effective search space used: 2421693000
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: 61 (27.4 bits)