RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1562
(620 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 = 426 bits (1098), Expect = e-147
Identities = 135/250 (54%), Positives = 175/250 (70%), Gaps = 2/250 (0%)
Query: 202 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 261
PQMI LTFD A+N NN + Y+K+F+ R NPNGCP+KGTFF+SHEY++Y +Q L +GH
Sbjct: 1 PQMITLTFDDAINDNNIELYKKIFNGKRNNPNGCPIKGTFFVSHEYTNYQAVQKLHRKGH 60
Query: 262 EIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNTQFE 321
EI V +I+ D + YE+WV EM+GMREIL FANIT ++IVGMRAPFL G N QFE
Sbjct: 61 EIAVHSITHNDDENNATYEDWVKEMVGMREILEKFANITDNEIVGMRAPFLRVGGNRQFE 120
Query: 322 VVEDFGFIYDSSVSVPALKFPVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLNAHFVES 381
++E+FGF+YDSS++ P P+WPYTLD+K+PHEC CPT+SFPGVWE+ LN V
Sbjct: 121 MMEEFGFLYDSSITAPPSNVPLWPYTLDYKMPHECHGQNCPTRSFPGVWEMVLNELDVRD 180
Query: 382 YEGGHCPY-LDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIK-ELEQG 439
G P +D L+ D+V EWL+ +F ++Y N+APY + FHTNW + K EL +
Sbjct: 181 DPQGDEPLAMDDSCLNILSGDQVYEWLQHNFERHYLTNRAPYGLYFHTNWLKTKNELLRA 240
Query: 440 LHKFLDWAAQ 449
L KFLD Q
Sbjct: 241 LQKFLDEILQ 250
Score = 43.5 bits (103), Expect = 2e-04
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 519 KPDVWFVTITQALTWMTNP 537
PDV+FVT+TQA+ WM NP
Sbjct: 251 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 = 261 bits (670), Expect = 3e-83
Identities = 116/272 (42%), Positives = 154/272 (56%), Gaps = 18/272 (6%)
Query: 202 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 261
PQ++ LTFD AVN NY +Y+K+F +RKNPNGCP+ TFF+SHEY+DY ++Q L N GH
Sbjct: 1 PQLVTLTFDDAVNTLNYPYYEKLF-GNRKNPNGCPIGATFFVSHEYTDYRLVQELYNDGH 59
Query: 262 EIGVETIS---LQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNT 318
EI + +IS QD ++ +EW E G REIL HFANI DI G RAPFL G +
Sbjct: 60 EIALHSISHRSPQDYWRNASVDEWEREFGGQREILAHFANIPAEDIKGFRAPFLQLGGDA 119
Query: 319 QFEVVEDFGFIYDSSVSVPALKF---PVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLN 375
F+ ++ G YDS S P F P+WPYTLD+ +C CPT S+PG W VP+
Sbjct: 120 TFKALKQLGLTYDS--SWPTQSFTNPPLWPYTLDYGSTQDCVIPPCPTDSYPGFWVVPMV 177
Query: 376 AHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWF-QIK 434
+ G C L C +DEV +WL +F ++Y N+AP+ + H +WF
Sbjct: 178 D--WQDLNGVPCSMLAACPPPG-TADEVYDWLLSNFERHYNTNRAPFGLYLHASWFEFTP 234
Query: 435 ELEQGLHKFLDWAAQNTLHDAIPHQLVPNQRA 466
+G KFLD +L D LV +A
Sbjct: 235 NRLEGFKKFLDEL--LSLDDVY---LVTISQA 261
Score = 35.0 bits (81), Expect = 0.086
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 517 TSKPDVWFVTITQALTWMTNP 537
S DV+ VTI+QA+ WM NP
Sbjct: 248 LSLDDVYLVTISQAIEWMRNP 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 = 216 bits (551), Expect = 1e-65
Identities = 91/256 (35%), Positives = 129/256 (50%), Gaps = 10/256 (3%)
Query: 202 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 261
PQ +L TFD A+N N D + +D N GCP+ TFF+S Y+D S+++ L GH
Sbjct: 1 PQFVLFTFDDAINELNTDAVIQEIADGTNNNGGCPIPATFFVSTNYTDCSLVKQLWREGH 60
Query: 262 EIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNTQFE 321
EI T++ + +EW E+ G RE L+ I +VG RAP+L NT E
Sbjct: 61 EIATHTVTHVPDDSNASVDEWEEEIAGQREWLNKTCGIPLEKVVGFRAPYLAYNPNT-RE 119
Query: 322 VVEDFGFIYDSSVSVPALKF---PVWPYTLDHKIPHECKSGTC---PTKSFPGVWEVPLN 375
V+E+ GF+YDSS+ P +WPYTLD+ IP +C PT+ +PG+WEVPL
Sbjct: 120 VLEENGFLYDSSIPEPYTPSGTNRLWPYTLDYGIPQDCNLVPGSCSPTERYPGLWEVPLY 179
Query: 376 AHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIKE 435
+ G Y + D LK +F+++Y N+AP+ + H W
Sbjct: 180 TLQDGNDTTG-DSYYCTPDDGPLNGDSFYALLKYNFDRHYNGNRAPFGIYLHAAWLSPPY 238
Query: 436 LE--QGLHKFLDWAAQ 449
E L KFLD+A
Sbjct: 239 SERRAALEKFLDYALS 254
Score = 37.7 bits (88), Expect = 0.010
Identities = 15/20 (75%), Positives = 16/20 (80%)
Query: 518 SKPDVWFVTITQALTWMTNP 537
SKPDVWFVT +Q L WM NP
Sbjct: 254 SKPDVWFVTNSQLLDWMQNP 273
>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 = 55.0 bits (133), Expect = 2e-08
Identities = 39/150 (26%), Positives = 63/150 (42%), Gaps = 28/150 (18%)
Query: 237 MKGTFF----ISHEYSDYSMIQNLANRGHEIGVETIS--LQDGLQDKGYEEWVGEMIGMR 290
+K TFF ++ Y D +I+ +A GHEI + D L + + E +R
Sbjct: 46 VKATFFVLGEVAERYPD--LIRRIAEAGHEIASHGYAHERVDRLTPEEFRE------DLR 97
Query: 291 EILHHFANITRSDIVGMRAPFLLPGRNTQ--FEVVEDFGFIYDSSVSVPALKFPVWPYTL 348
+IT +VG RAP T +++ + G++YDSSV FP
Sbjct: 98 RSKKILEDITGQKVVGFRAPNF---SITPWALDILAEAGYLYDSSV------FPTKRP-- 146
Query: 349 DHKIPHECKSGT-CPTKSFPGVWEVPLNAH 377
+ P KS P ++ G+ E P++
Sbjct: 147 GYGGPLAPKSEPLPPIRAKGGILEFPVSVT 176
>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 = 43.9 bits (104), Expect = 1e-04
Identities = 60/291 (20%), Positives = 92/291 (31%), Gaps = 97/291 (33%)
Query: 202 PQMILLTFDGAVNLNNYDHYQKVFSDSRK--NPNGCPMKGTFFISHEY-------SDY-- 250
PQ ++ +FDGA D+ +++S SR T+F+S Y + Y
Sbjct: 2 PQFVVFSFDGA-----GDN--QLWSRSRAVAKQTNARF--TYFLSGVYLLTTENRTLYTP 52
Query: 251 ----------------SMIQ------NLANR-GHEIGVETISLQDG---LQDKGYEEWVG 284
+ N A R GHEIG DG +W
Sbjct: 53 PGQKAGRSNIGFAGSRQEVADRLRQLNAAYREGHEIGSHANGHFDGKGGGGRWSVADWKR 112
Query: 285 EMIGMREILHHFANIT------------RSDIVGMRAPFLLPGRNTQFEVVEDFGFIYDS 332
E + + I + I G RAP L + Q ++ GF YD+
Sbjct: 113 EFDQFYRFVENAYAINGIEGAPPWPAFAPNSIKGFRAPCLEGSKGLQ-PALKKHGFTYDA 171
Query: 333 SVSVPALKFPVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLNAHFVESYEGGHCPYL-- 390
S SV + P WP +D G+W PL P +
Sbjct: 172 S-SVT--QGPYWPQKVD------------------GIWNFPLPL---VPEGPTSRPVIAM 207
Query: 391 --DQCVLHNHDSDE----------VLEWLKEDFNKYYTQNKAPYMMPFHTN 429
+ V H+ + +L + F++ Y N+AP + H
Sbjct: 208 DYNLFVRHSGGVEAPAKAAEFEARMLATYRNAFDRAYNGNRAPLQLGNHFV 258
>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 = 36.6 bits (85), Expect = 0.001
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 477 GCSK---CVDHHPYVSLCPSGLYFDDIKKLCTFKNEAR 511
CSK C + V CP+GL FD C + +
Sbjct: 14 DCSKYYQCSNGKAVVFTCPAGLVFDPALGTCDYPDNVV 51
>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 = 38.9 bits (91), Expect = 0.005
Identities = 24/117 (20%), Positives = 51/117 (43%), Gaps = 28/117 (23%)
Query: 238 KGTFF----ISHEYSDYSMIQNLANRGHEI-----GVETISLQDGLQDKGYEEWVGEMIG 288
K TFF ++ Y + +++ + GHE+ G E ++ Q E + ++
Sbjct: 49 KATFFTLGWVAERYPE--LVRRIVAAGHELASHGYGHERVTTQTP------EAFRADIRR 100
Query: 289 MREILHHFANITRSDIVGMRAPFLLPGRNT--QFEVVEDFGFIYDSSVSVPALKFPV 343
+ +L +++ + G RAP G+ +V+ + G+ Y SS+ +P+
Sbjct: 101 SKALLE---DLSGQPVRGYRAPSFSIGKKNLWALDVLAEAGYRYSSSI------YPI 148
>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 = 37.4 bits (87), Expect = 0.005
Identities = 23/120 (19%), Positives = 38/120 (31%), Gaps = 17/120 (14%)
Query: 204 MILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSM----------I 253
++LLT D G + T F+ ++ +
Sbjct: 1 LVLLTLDDDPAFEGS---PAALQRLLDLLEGYGIPATLFVIPGNANPDKLMKSPLNWDLL 57
Query: 254 QNLANRGHEIGVETISLQDGLQ-DKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFL 312
+ L GHEIG+ + D + EE + +++ R IL G RAP
Sbjct: 58 RELLAYGHEIGLHGYTHPDLAYGNLSPEEVLEDLLRARRIL---EEAGGQPPKGFRAPGG 114
>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 = 37.7 bits (88), Expect = 0.007
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 237 MKGTFFIS------HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMR 290
+KGTFF++ Y D ++ LA GHEIG T++ D L E E+ R
Sbjct: 26 LKGTFFVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPD-LTSLPPAELRREIAESR 84
Query: 291 EILH 294
L
Sbjct: 85 AALE 88
>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 = 37.9 bits (89), Expect = 0.009
Identities = 29/111 (26%), Positives = 45/111 (40%), Gaps = 31/111 (27%)
Query: 237 MKGTFFIS----HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYE-EWVGEMIGM-- 289
+K TFF+ + + ++ + GHEIG GY E G+
Sbjct: 51 VKATFFVPGHTAETFPE--AVEAILAAGHEIGHH-----------GYLHENP---TGLTP 94
Query: 290 ---REILHH----FANITRSDIVGMRAPFLLPGRNTQFEVVEDFGFIYDSS 333
RE+L +T VG R+P NT +++ + GF+YDSS
Sbjct: 95 EEERELLERGLELLEKLTGKRPVGYRSPSWEFSPNT-LDLLLEHGFLYDSS 144
>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 = 36.1 bits (84), Expect = 0.013
Identities = 31/136 (22%), Positives = 50/136 (36%), Gaps = 15/136 (11%)
Query: 197 DAEDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFF-ISHEYSDY-SMIQ 254
+ + + LTFD D+ ++ +K +K TFF I Y +++
Sbjct: 1 KGDTPKKSVALTFDDGPP----DNTPRILDVLKKYG----VKATFFVIGGNAETYPDLVR 52
Query: 255 NLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLP 314
+ GHEIG T S D L EE E++ +E + T R P+
Sbjct: 53 RMVAEGHEIGNHTWSHPD-LTALSPEEIRAEILRSQEAI---KKATGKRPRLFRPPYGSY 108
Query: 315 GRNTQFEVVEDFGFIY 330
+T + G Y
Sbjct: 109 NDDT-LAAAKKLGLRY 123
>gnl|CDD|214696 smart00494, ChtBD2, Chitin-binding domain type 2.
Length = 49
Score = 31.6 bits (72), Expect = 0.078
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 478 CSK---CVDHHPYVSLCPSGLYFDDIKKLCTFK 507
CSK C + P V CP+GL F+ + C +
Sbjct: 17 CSKYYQCSNGRPIVGSCPAGLVFNPATQTCDWP 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 = 33.8 bits (78), Expect = 0.17
Identities = 28/117 (23%), Positives = 40/117 (34%), Gaps = 18/117 (15%)
Query: 201 TPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFIS-----HEYSDY-SMIQ 254
P + LTFD Y D K K TFF++ DY +++
Sbjct: 6 VPGTVALTFDDG-----PSTYTPQLLDLLKEAG---AKATFFVNGNNFNGCIYDYADVLR 57
Query: 255 NLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPF 311
+ N GH+I T S D L + EM + + I MR P+
Sbjct: 58 RMYNEGHQIASHTWSHPD-LTKLSAAQIRDEMTKLED---ALRKILGVKPTYMRPPY 110
>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 = 31.8 bits (73), Expect = 0.56
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 237 MKGTFFIS----HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREI 292
+K TFF+ ++ D +++ + GHEIG T S L EE E+ ++
Sbjct: 28 VKATFFVVGENVEKHPD--LVRRIVAEGHEIGNHTYS-HPDLTKLSPEEIRAEIERTQDA 84
Query: 293 LHHFANITRSDIVGMRAPF 311
+ T R P+
Sbjct: 85 I---EEATGVRPRLFRPPY 100
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 32.4 bits (73), Expect = 0.92
Identities = 22/75 (29%), Positives = 26/75 (34%), Gaps = 13/75 (17%)
Query: 40 AAHQMTYNRP--PEYYYDDTTHQQMPVLPQPHSLNNMDMAAHQMTYNRPPEYYYDDTTHQ 97
A Q Y +P P Q PV PQP A Q Y +P
Sbjct: 785 VAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQP----------- 833
Query: 98 QMPVLPQPHSNIIPP 112
Q PV PQP ++ P
Sbjct: 834 QQPVAPQPQDTLLHP 848
>gnl|CDD|224373 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 467
Score = 31.7 bits (72), Expect = 1.4
Identities = 30/145 (20%), Positives = 55/145 (37%), Gaps = 22/145 (15%)
Query: 176 SSCTLPYCFCSKDGTIIPGGLDAEDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGC 235
+ LP CS D ++ L+ + +L A +N+ + K+ +
Sbjct: 156 AEAGLPVILCSFDPEVMKAALEVVKDQKPLLY----AATEDNWKEFAKLAVEY-----KV 206
Query: 236 PMKGTFFISHEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHH 295
P+ + ++D ++NLA + G++ I L G GE G+++ +
Sbjct: 207 PL-----VLSAFNDLDDLKNLAVTYAQAGIKDIVLDPG------TYPGGE--GLKDTFDN 253
Query: 296 FANITRSDIVGMRAPFLLPGRNTQF 320
F I R+ I G F P F
Sbjct: 254 FVMIRRAAIEGFDKDFAYPIMALPF 278
>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 = 30.7 bits (70), Expect = 2.1
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 22/98 (22%)
Query: 242 FISHEYSDY-SMIQNLANRGHEIGV----ETISLQDGLQDKGYEEWVGEMIGMREILHHF 296
S+ S+I+ +A+RG EIG+ + + + L+ E + +IL
Sbjct: 46 NYSYNDPKIRSLIKEIADRGWEIGLHGSYNSYTDPEKLKK--------EKERLEKILGR- 96
Query: 297 ANITRSDIVGMRAPFL-LPGRNTQFEVVEDFGFIYDSS 333
+ G R +L T + + D GF YDS+
Sbjct: 97 ------PVTGGRQHYLRFDLPET-WRNLADAGFTYDST 127
>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 = 29.8 bits (67), Expect = 3.1
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 240 TFFISHEYS-DY-SMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFA 297
TFF+ Y+ ++ +I+ + GHE+G T++ D L E E+ +++ H
Sbjct: 31 TFFVIGAYAAEHPELIRRMIAEGHEVGNHTMTHPD-LSRCEPGEVQREISSANKVIRHAC 89
Query: 298 NITRSDIVGMRAPF 311
R+ + RAP+
Sbjct: 90 --PRASVRYFRAPY 101
>gnl|CDD|224150 COG1229, FwdA, Formylmethanofuran dehydrogenase subunit A [Energy
production and conversion].
Length = 575
Score = 30.1 bits (68), Expect = 3.9
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 397 NHDSDEVLEWLKEDFNKYYTQNKAPYMMP 425
+E+L+ ++E F KYYT N A Y +
Sbjct: 531 ESLMEEMLKDVEEKFRKYYTVNLANYPVE 559
>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 = 29.4 bits (67), Expect = 4.0
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 237 MKGTFF-ISHEYSDY-SMIQNLANRGHEIGVETIS 269
+K TFF I Y +++ + GH IG+ + +
Sbjct: 27 VKATFFVIGSNVEKYPELVKRIVKEGHAIGLHSYT 61
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 29.9 bits (68), Expect = 4.2
Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 20/92 (21%)
Query: 240 TFFISHEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANI 299
H I GHEI E + + DG G++ +G R +
Sbjct: 43 KIRGGHTDLKPPRIL-----GHEIAGEIVEVGDG--VTGFK------VGDRVFVAPH--- 86
Query: 300 TRSDIVGMRAPFLLPGRNTQFEVVEDFGFIYD 331
+ + L G + FG +YD
Sbjct: 87 ----VPCGECHYCLRGNENMCPNYKKFGNLYD 114
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 28.0 bits (63), Expect = 4.8
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 390 LDQCVLHNHDSDEVLEW----LKEDFNKYYT 416
L+Q +D+DE LE+ L DF ++Y
Sbjct: 13 LEQTQRDEYDTDEGLEYDEEDLYSDFEEFYD 43
>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 = 29.6 bits (67), Expect = 4.9
Identities = 34/113 (30%), Positives = 42/113 (37%), Gaps = 27/113 (23%)
Query: 253 IQNLANRGHEI---GVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRA 309
+ + GHEI G I Q + EE RE + I + G R
Sbjct: 92 ARAMVAAGHEIASHGWRWIDYQGMDEA---EE--------REHIRRAIAIIE-RLTGERP 139
Query: 310 PFLLPGR---NTQFEVVEDFGFIYDSS---------VSVPALKFPVWPYTLDH 350
GR NT+ VVE+ GF+YDS V V V PYTLD
Sbjct: 140 LGWYTGRASPNTRRLVVEEGGFLYDSDSYDDDLPYWVDVEGKPHLVVPYTLDT 192
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.7 bits (66), Expect = 5.4
Identities = 18/110 (16%), Positives = 35/110 (31%), Gaps = 10/110 (9%)
Query: 20 VPAYQHVAPVQNSGLNNMDMAAHQMTYNRPPEYYYDDTTHQQMPVLPQPHSLNNMDMAAH 79
VP + + NS +N +M + N + + P + + +
Sbjct: 182 VPHNKQINSNNNSTSHNSNMGSKNAKMNDSSKL----KKLSLIEEKKFPERVRSRYIDIG 237
Query: 80 QMTYNRPPEYYYDDTTHQQMPVLPQPHSN----IIPPSVGSYQSWTTEVL 125
M ++Y +D +L + I PS GS + + L
Sbjct: 238 HMMDT--HQFYLEDVDLMDDDILGPSNEEMLYKYISPSQGSAELFEESSL 285
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 29.6 bits (67), Expect = 6.5
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 236 PMKGTFFISHEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGE 285
P GT FIS D + LA R ++G + ++ +G W+ E
Sbjct: 935 PSYGTIFISVRDEDKPEVTKLARRFAQLGFKLLA------TEGTANWLAE 978
>gnl|CDD|237236 PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
Length = 340
Score = 29.2 bits (66), Expect = 6.7
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 371 EVPLNAHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKE 409
EVP++ FVE ++G Y +E + +E
Sbjct: 206 EVPVDMKFVEGFDGFEEAY---------TQEEAFKLFRE 235
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 29.4 bits (66), Expect = 7.0
Identities = 15/100 (15%), Positives = 22/100 (22%), Gaps = 17/100 (17%)
Query: 21 PAYQHVAPVQNSGLNNMDMAAHQMTYNRPPEYYYDDTTHQQMPVLPQPHSLNNMDMAAHQ 80
P + + Q VLPQ
Sbjct: 146 PQTPAQKMLSLEEVEAQLQQRQQA----------PQLPQPPQQVLPQGMPPRQAAFPQQG 195
Query: 81 MT-----YNRPPEYYYDDTTHQQMPVLP--QPHSNIIPPS 113
Y +PP+ + + QQ P P +PP
Sbjct: 196 PPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQ 235
>gnl|CDD|184749 PRK14566, PRK14566, triosephosphate isomerase; Provisional.
Length = 260
Score = 28.7 bits (64), Expect = 7.7
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 478 CSKCVDHHPYVSLCPSGLYFDDIKKLCTFKNEARCGPL 515
K + V LCP +Y + +++L EA G L
Sbjct: 29 AGKLQNDSAEVVLCPPSIYLESVRQLLEANKEALDGSL 66
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.436
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: 31,722,687
Number of extensions: 3008988
Number of successful extensions: 2203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2182
Number of HSP's successfully gapped: 37
Length of query: 620
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 517
Effective length of database: 6,369,140
Effective search space: 3292845380
Effective search space used: 3292845380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.8 bits)