RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10480
(435 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 = 466 bits (1201), Expect = e-166
Identities = 147/269 (54%), Positives = 188/269 (69%), Gaps = 5/269 (1%)
Query: 121 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 180
PQMI LTFD A+N NN + Y+K+F+ R NPNGCP+KGTFF+SHEY++Y +Q L +GH
Sbjct: 1 PQMITLTFDDAINDNNIELYKKIFNGKRNNPNGCPIKGTFFVSHEYTNYQAVQKLHRKGH 60
Query: 181 EIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNTQFE 240
EI V +I+ D + YE+WV EM+GMREIL FANIT ++IVGMRAPFL G N QFE
Sbjct: 61 EIAVHSITHNDDENNATYEDWVKEMVGMREILEKFANITDNEIVGMRAPFLRVGGNRQFE 120
Query: 241 ---DFGFIYDSSVSVPALKFPVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLNAHFVES 297
+FGF+YDSS++ P P+WPYTLD+K+PHEC CPT+SFPGVWE+ LN V
Sbjct: 121 MMEEFGFLYDSSITAPPSNVPLWPYTLDYKMPHECHGQNCPTRSFPGVWEMVLNELDVRD 180
Query: 298 YEGGHCPY-LDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIK-ELEQG 355
G P +D L+ D+V EWL+ +F ++Y N+APY + FHTNW + K EL +
Sbjct: 181 DPQGDEPLAMDDSCLNILSGDQVYEWLQHNFERHYLTNRAPYGLYFHTNWLKTKNELLRA 240
Query: 356 LHKFLDWAAQKPDVWFVTITQALTWMTNP 384
L KFLD Q PDV+FVT+TQA+ WM NP
Sbjct: 241 LQKFLDEILQLPDVYFVTMTQAIQWMQNP 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 = 289 bits (743), Expect = 2e-96
Identities = 122/274 (44%), Positives = 159/274 (58%), Gaps = 16/274 (5%)
Query: 121 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 180
PQ++ LTFD AVN NY +Y+K+F +RKNPNGCP+ TFF+SHEY+DY ++Q L N GH
Sbjct: 1 PQLVTLTFDDAVNTLNYPYYEKLF-GNRKNPNGCPIGATFFVSHEYTDYRLVQELYNDGH 59
Query: 181 EIGVETIS---LQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNT 237
EI + +IS QD ++ +EW E G REIL HFANI DI G RAPFL G +
Sbjct: 60 EIALHSISHRSPQDYWRNASVDEWEREFGGQREILAHFANIPAEDIKGFRAPFLQLGGDA 119
Query: 238 QFE---DFGFIYDSSVSVPALKF---PVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLN 291
F+ G YDS S P F P+WPYTLD+ +C CPT S+PG W VP+
Sbjct: 120 TFKALKQLGLTYDS--SWPTQSFTNPPLWPYTLDYGSTQDCVIPPCPTDSYPGFWVVPMV 177
Query: 292 AHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWF-QIK 350
+ G C L C +DEV +WL +F ++Y N+AP+ + H +WF
Sbjct: 178 D--WQDLNGVPCSMLAACPPPG-TADEVYDWLLSNFERHYNTNRAPFGLYLHASWFEFTP 234
Query: 351 ELEQGLHKFLDWAAQKPDVWFVTITQALTWMTNP 384
+G KFLD DV+ VTI+QA+ WM NP
Sbjct: 235 NRLEGFKKFLDELLSLDDVYLVTISQAIEWMRNP 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 = 248 bits (634), Expect = 5e-80
Identities = 103/274 (37%), Positives = 142/274 (51%), Gaps = 11/274 (4%)
Query: 121 PQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSMIQNLANRGH 180
PQ +L TFD A+N N D + +D N GCP+ TFF+S Y+D S+++ L GH
Sbjct: 1 PQFVLFTFDDAINELNTDAVIQEIADGTNNNGGCPIPATFFVSTNYTDCSLVKQLWREGH 60
Query: 181 EIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLPGRNTQ-- 238
EI T++ + +EW E+ G RE L+ I +VG RAP+L NT+
Sbjct: 61 EIATHTVTHVPDDSNASVDEWEEEIAGQREWLNKTCGIPLEKVVGFRAPYLAYNPNTREV 120
Query: 239 FEDFGFIYDSSVSVPALKF---PVWPYTLDHKIPHECKSGTC---PTKSFPGVWEVPLNA 292
E+ GF+YDSS+ P +WPYTLD+ IP +C PT+ +PG+WEVPL
Sbjct: 121 LEENGFLYDSSIPEPYTPSGTNRLWPYTLDYGIPQDCNLVPGSCSPTERYPGLWEVPLYT 180
Query: 293 HFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIKEL 352
+ G Y + D LK +F+++Y N+AP+ + H W
Sbjct: 181 LQDGNDTTG-DSYYCTPDDGPLNGDSFYALLKYNFDRHYNGNRAPFGIYLHAAWLSPPYS 239
Query: 353 E--QGLHKFLDWAAQKPDVWFVTITQALTWMTNP 384
E L KFLD+A KPDVWFVT +Q L WM NP
Sbjct: 240 ERRAALEKFLDYALSKPDVWFVTNSQLLDWMQNP 273
>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 = 54.0 bits (130), Expect = 7e-10
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 19 CPDEGGNGNYADPSTCRRFYQCVDHHPYVSLCPSGLYFDDIKKLCTFKNEAR 70
C +G Y DP C ++YQC + V CP+GL FD C + +
Sbjct: 1 CEGRP-DGLYPDPGDCSKYYQCSNGKAVVFTCPAGLVFDPALGTCDYPDNVV 51
>gnl|CDD|214696 smart00494, ChtBD2, Chitin-binding domain type 2.
Length = 49
Score = 50.5 bits (121), Expect = 1e-08
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 17 FVCPDEGGNGNYADPSTCRRFYQCVDHHPYVSLCPSGLYFDDIKKLCTFK 66
CP G+G Y P+ C ++YQC + P V CP+GL F+ + C +
Sbjct: 1 NECP-GRGDGLYPHPTDCSKYYQCSNGRPIVGSCPAGLVFNPATQTCDWP 49
>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 = 49.3 bits (118), Expect = 2e-06
Identities = 67/326 (20%), Positives = 106/326 (32%), Gaps = 98/326 (30%)
Query: 121 PQMILLTFDGAVNLNNYDHYQKVFSDSRK--NPNGCPMKGTFFISHEY-------SDY-- 169
PQ ++ +FDGA D+ +++S SR T+F+S Y + Y
Sbjct: 2 PQFVVFSFDGA-----GDN--QLWSRSRAVAKQTNARF--TYFLSGVYLLTTENRTLYTP 52
Query: 170 ----------------SMIQ------NLANR-GHEIGVETISLQDG---LQDKGYEEWVG 203
+ N A R GHEIG DG +W
Sbjct: 53 PGQKAGRSNIGFAGSRQEVADRLRQLNAAYREGHEIGSHANGHFDGKGGGGRWSVADWKR 112
Query: 204 EMIGMREILHHFANIT------------RSDIVGMRAPFLLPGRNTQ--FEDFGFIYDSS 249
E + + I + I G RAP L + Q + GF YD+S
Sbjct: 113 EFDQFYRFVENAYAINGIEGAPPWPAFAPNSIKGFRAPCLEGSKGLQPALKKHGFTYDAS 172
Query: 250 VSVPALKFPVWPYTLDHKIPHECKSGTCPTKSFPGVWEVPLNAHFVESYEGGHCPYL--- 306
SV + P WP +D G+W PL P +
Sbjct: 173 -SVT--QGPYWPQKVD------------------GIWNFPLPL---VPEGPTSRPVIAMD 208
Query: 307 -DQCVLHNHDSDE----------VLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIKELEQG 355
+ V H+ + +L + F++ Y N+AP + H +
Sbjct: 209 YNLFVRHSGGVEAPAKAAEFEARMLATYRNAFDRAYNGNRAPLQLGNHFVKWNGGAYWNA 268
Query: 356 LHKFLDWAAQKPDVWFVTITQALTWM 381
L +F + KP+V VT + + ++
Sbjct: 269 LERFAEEVCTKPEVKCVTYRELVDFL 294
>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 = 48.1 bits (115), Expect = 3e-06
Identities = 38/149 (25%), Positives = 59/149 (39%), Gaps = 29/149 (19%)
Query: 156 MKGTFF----ISHEYSDYSMIQNLANRGHEIGVETIS--LQDGLQDKGYEEWVGEMIGMR 209
+K TFF ++ Y D +I+ +A GHEI + D L + + E +R
Sbjct: 46 VKATFFVLGEVAERYPD--LIRRIAEAGHEIASHGYAHERVDRLTPEEFRE------DLR 97
Query: 210 EILHHFANITRSDIVGMRAPFLLPGRNTQF----EDFGFIYDSSVSVPALKFPVWPYTLD 265
+IT +VG RAP + G++YDSSV FP
Sbjct: 98 RSKKILEDITGQKVVGFRAPNF--SITPWALDILAEAGYLYDSSV------FPTKRP--G 147
Query: 266 HKIPHECKSGT-CPTKSFPGVWEVPLNAH 293
+ P KS P ++ G+ E P++
Sbjct: 148 YGGPLAPKSEPLPPIRAKGGILEFPVSVT 176
>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 = 39.8 bits (94), Expect = 0.002
Identities = 49/248 (19%), Positives = 81/248 (32%), Gaps = 79/248 (31%)
Query: 156 MKGTFFIS----HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYE-EWVGEMIGM-- 208
+K TFF+ + + ++ + GHEIG GY E G+
Sbjct: 51 VKATFFVPGHTAETFPE--AVEAILAAGHEIGHH-----------GYLHENP---TGLTP 94
Query: 209 ---REILHH----FANITRSDIVGMRAPF--LLPGRNTQFEDFGFIYDSSVSVPALKFPV 259
RE+L +T VG R+P P + GF+YDSS
Sbjct: 95 EEERELLERGLELLEKLTGKRPVGYRSPSWEFSPNTLDLLLEHGFLYDSS---------- 144
Query: 260 WPYTLDHKIPHECKSGTCPTKSFPGVWEVPLN------AHFVESYEG-GHCPYLDQCVLH 312
+ P+ T G+ E+P++ +F + G
Sbjct: 145 ---LMGDDRPYYYVRRGEET----GLVEIPVHWELDDFPYFAFNRSPPGPPGI------- 190
Query: 313 NHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQ-------IKELEQGLHKFLDWAAQ 365
+VL+ K++F+ Y + + + H Q I LE + ++
Sbjct: 191 -APPRDVLDNWKDEFDGAYEEGGV-FTLTLHP---QVIGRPSRIAMLE----RLIEHIKA 241
Query: 366 KPDVWFVT 373
VWF T
Sbjct: 242 HGGVWFAT 249
>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 = 38.2 bits (89), Expect = 0.002
Identities = 23/120 (19%), Positives = 38/120 (31%), Gaps = 17/120 (14%)
Query: 123 MILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYSM----------I 172
++LLT D G + T F+ ++ +
Sbjct: 1 LVLLTLDDDPAFEGS---PAALQRLLDLLEGYGIPATLFVIPGNANPDKLMKSPLNWDLL 57
Query: 173 QNLANRGHEIGVETISLQDGLQ-DKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFL 231
+ 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 = 38.1 bits (89), Expect = 0.004
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 156 MKGTFFIS------HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMR 209
+KGTFF++ Y D ++ LA GHEIG T++ D L E E+ R
Sbjct: 26 LKGTFFVNSGLLGRRGYLDLEELRELAAAGHEIGSHTVTHPD-LTSLPPAELRREIAESR 84
Query: 210 EILH 213
L
Sbjct: 85 AALE 88
>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 = 35.3 bits (82), Expect = 0.012
Identities = 29/124 (23%), Positives = 47/124 (37%), Gaps = 14/124 (11%)
Query: 116 DAEDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFF-ISHEYSDY-SMIQ 173
+ + + LTFD D+ ++ +K +K TFF I Y +++
Sbjct: 1 KGDTPKKSVALTFDDGPP----DNTPRILDVLKKYG----VKATFFVIGGNAETYPDLVR 52
Query: 174 NLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPFLLP 233
+ GHEIG T S D L EE E++ +E + T R P+
Sbjct: 53 RMVAEGHEIGNHTWSHPD-LTALSPEEIRAEILRSQEAI---KKATGKRPRLFRPPYGSY 108
Query: 234 GRNT 237
+T
Sbjct: 109 NDDT 112
>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 = 34.6 bits (80), Expect = 0.051
Identities = 28/117 (23%), Positives = 40/117 (34%), Gaps = 18/117 (15%)
Query: 120 TPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFIS-----HEYSDY-SMIQ 173
P + LTFD Y D K K TFF++ DY +++
Sbjct: 6 VPGTVALTFDDG-----PSTYTPQLLDLLKEAG---AKATFFVNGNNFNGCIYDYADVLR 57
Query: 174 NLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAPF 230
+ N GH+I T S D L + EM + + I MR P+
Sbjct: 58 RMYNEGHQIASHTWSHPD-LTKLSAAQIRDEMTKLED---ALRKILGVKPTYMRPPY 110
>gnl|CDD|224373 COG1456, CdhE, CO dehydrogenase/acetyl-CoA synthase gamma subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 467
Score = 35.2 bits (81), Expect = 0.062
Identities = 34/157 (21%), Positives = 60/157 (38%), Gaps = 22/157 (14%)
Query: 95 SSCTLPYCFCSKDGTIIPGGLDAEDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGC 154
+ LP CS D ++ L+ + +L A +N+ + K+ +
Sbjct: 156 AEAGLPVILCSFDPEVMKAALEVVKDQKPLLY----AATEDNWKEFAKLAVEY-----KV 206
Query: 155 PMKGTFFISHEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHH 214
P+ + ++D ++NLA + G++ I L G GE G+++ +
Sbjct: 207 PL-----VLSAFNDLDDLKNLAVTYAQAGIKDIVLDPG------TYPGGE--GLKDTFDN 253
Query: 215 FANITRSDIVGMRAPFLLPGRNTQFEDFGFIYDSSVS 251
F I R+ I G F P F + F D VS
Sbjct: 254 FVMIRRAAIEGFDKDFAYPIMALPFTAWMFGEDDPVS 290
>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 = 34.2 bits (79), Expect = 0.10
Identities = 23/117 (19%), Positives = 49/117 (41%), Gaps = 31/117 (26%)
Query: 157 KGTFF----ISHEYSDYSMIQNLANRGHEI-----GVETISLQDGLQDKGYEEWVGEMIG 207
K TFF ++ Y + +++ + GHE+ G E ++ Q E + ++
Sbjct: 49 KATFFTLGWVAERYPE--LVRRIVAAGHELASHGYGHERVTTQTP------EAFRADIRR 100
Query: 208 MREILHHFANITRSDIVGMRAPFLLPGRNTQF-----EDFGFIYDSSVSVPALKFPV 259
+ +L +++ + G RAP G+ + + G+ Y SS+ +P+
Sbjct: 101 SKALLE---DLSGQPVRGYRAPSFSIGKKNLWALDVLAEAGYRYSSSI------YPI 148
>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 = 32.6 bits (75), Expect = 0.21
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 156 MKGTFFIS----HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREI 211
+K TFF+ ++ D +++ + GHEIG T S L EE E+ ++
Sbjct: 28 VKATFFVVGENVEKHPD--LVRRIVAEGHEIGNHTYS-HPDLTKLSPEEIRAEIERTQDA 84
Query: 212 LHHFANITRSDIVGMRAPF 230
+ T R P+
Sbjct: 85 I---EEATGVRPRLFRPPY 100
>gnl|CDD|200601 cd10979, CE4_PuuE_like, Putative catalytic domain of
uncharacterized prokaryotic polysaccharide deacetylases
similar to bacterial PuuE allantoinases. The family
includes a group of uncharacterized prokaryotic
polysaccharide deacetylases (DCAs) that show high
sequence similarity 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 DCA-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
DCAs which are normally metal ion dependent and
recognize multimeric substrates.
Length = 281
Score = 32.6 bits (75), Expect = 0.32
Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 309 CVLHNHDSDEVLEWLKEDFNKYYTQ-NKAPYMMPF--HTNW-----FQIKELEQGLHKFL 360
++ H +DE + + + F++ Y + ++ +M H + +I+ LE + L
Sbjct: 203 YLVRGHSADEFADRIIDQFDQLYAEGAESGRVMAIALHP-YIVGQPHRIRALE----EAL 257
Query: 361 DWAAQKPDVWFVTITQALTWM 381
++ A PDVWF T + W
Sbjct: 258 EYIAAHPDVWFATGGEIADWF 278
>gnl|CDD|200602 cd10980, CE4_SpCDA1, Putative catalytic domain of
Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1),
and similar proteins. This family is represented by
Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1),
encoded by the cda1 gene. 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 be involved in allantoin hydrolysis. It is likely
an ortholog to bacterial 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 = 297
Score = 32.1 bits (73), Expect = 0.43
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 5/72 (6%)
Query: 315 DSDEVLEWLKEDFNKYYTQ--NKAPYMMP--FHTNWFQIKELEQGLHKFLDWAAQKPDVW 370
+SD+ +L++ F+ Y + AP MM H GL KF+++ K VW
Sbjct: 221 NSDDFYTYLRDAFDVLYEEGLEGAPKMMTIGLHCRITGRPGRFAGLRKFMEYITSKEGVW 280
Query: 371 FVTITQ-ALTWM 381
T + A W
Sbjct: 281 VATREEIAQAWS 292
>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 = 31.0 bits (71), Expect = 0.95
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 23/97 (23%)
Query: 161 FISHEYSDY-SMIQNLANRGHEIGV----ETISLQDGLQDKGYEEWVGEMIGMREILHHF 215
S+ S+I+ +A+RG EIG+ + + + L+ E + +IL
Sbjct: 46 NYSYNDPKIRSLIKEIADRGWEIGLHGSYNSYTDPEKLKK--------EKERLEKILGR- 96
Query: 216 ANITRSDIVGMRAPFL---LPGRNTQFEDFGFIYDSS 249
+ G R +L LP D GF YDS+
Sbjct: 97 ------PVTGGRQHYLRFDLPETWRNLADAGFTYDST 127
>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 = 30.9 bits (70), Expect = 1.0
Identities = 48/218 (22%), Positives = 74/218 (33%), Gaps = 59/218 (27%)
Query: 170 SMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFANITRSDIVGMRAP 229
+ + + RGHE Q+ +E G+ I +T VG A
Sbjct: 83 DLAKEIVQRGHEAAAHGRDWQNQFSMSREQERAFIQDGVDSIQ----KVTGQRPVGYNAF 138
Query: 230 FLLPGRNTQ--FEDFGFIY---DSS------VSVPALKFPVWPYTLDHKIPHECKSGTCP 278
+L NT ++ GF+Y D S + V F V PYTL
Sbjct: 139 WLRGSPNTLDILQELGFVYHIDDVSRDEPFIIPVNGKDFVVVPYTLR------------- 185
Query: 279 TKSFPGVWEVPLNAHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKEDFNKYYTQNKAPY 338
N + +EG + SD L+ LK++F++ Y + A +
Sbjct: 186 -----------NND--IVRFEGRA-----------YSSDAYLQELKDEFDQLYEE--AAH 219
Query: 339 ---MMP--FHTNWFQIKELEQGLHKFLDWAAQKPDVWF 371
MM H + + L +FL +A P V F
Sbjct: 220 RRRMMSISLHDRISGTPQRVRVLDEFLTYAKSHPGVTF 257
>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 = 1.7
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 159 TFFISHEYS-DY-SMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREILHHFA 216
TFF+ Y+ ++ +I+ + GHE+G T++ D L E E+ +++ H
Sbjct: 31 TFFVIGAYAAEHPELIRRMIAEGHEVGNHTMTHPD-LSRCEPGEVQREISSANKVIRHAC 89
Query: 217 NITRSDIVGMRAPF 230
R+ + RAP+
Sbjct: 90 --PRASVRYFRAPY 101
>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 = 29.8 bits (68), Expect = 1.9
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 156 MKGTFF-ISHEYSDY-SMIQNLANRGHEIGVETIS 188
+K TFF I Y +++ + GH IG+ + +
Sbjct: 27 VKATFFVIGSNVEKYPELVKRIVKEGHAIGLHSYT 61
>gnl|CDD|224150 COG1229, FwdA, Formylmethanofuran dehydrogenase subunit A [Energy
production and conversion].
Length = 575
Score = 30.5 bits (69), Expect = 2.0
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 313 NHDSDEVLEWLKEDFNKYYTQNKAPYMMP 341
+E+L+ ++E F KYYT N A Y +
Sbjct: 531 ESLMEEMLKDVEEKFRKYYTVNLANYPVE 559
>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 = 3.6
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 306 LDQCVLHNHDSDEVLEW----LKEDFNKYYT 332
L+Q +D+DE LE+ L DF ++Y
Sbjct: 13 LEQTQRDEYDTDEGLEYDEEDLYSDFEEFYD 43
>gnl|CDD|153339 cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Protein
kinase C and Casein kinase Substrate in Neurons (PACSIN)
proteins, also called Synaptic dynamin-associated
proteins (Syndapins), act as regulators of cytoskeletal
and membrane dynamics. They bind both dynamin and
Wiskott-Aldrich syndrome protein (WASP), and may provide
direct links between the actin cytoskeletal machinery
through WASP and dynamin-dependent endocytosis.
Vetebrates harbor three isoforms with distinct
expression patterns and specific functions. PACSINs
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 29.2 bits (66), Expect = 3.7
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 16/57 (28%)
Query: 311 LHNHDSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIKELEQGLHKFLDWAAQKP 367
L N +EV W KE+++K M + + KE E G K AQKP
Sbjct: 87 LLNDVVEEVKTWQKENYHK---------SMMGG--FKETKEAEDGFAK-----AQKP 127
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 29.6 bits (67), Expect = 3.8
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 155 PMKGTFFISHEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGE 204
P GT FIS D + LA R ++G + ++ +G W+ E
Sbjct: 935 PSYGTIFISVRDEDKPEVTKLARRFAQLGFKLLA------TEGTANWLAE 978
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 29.4 bits (65), Expect = 4.3
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 321 EWLKEDFNKYYTQNKAPYMMP---FHTNWFQ-IKELEQGLH--------KFLDWAAQK 366
++LKE K Y+Q K Y MP + + W Q IK ++QG +F +W QK
Sbjct: 208 DFLKEKLQKTYSQYKVQYDMPKEAYESKWGQCIKLIDQGGDNLEERLNSQFKNWYRQK 265
>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 = 28.5 bits (64), Expect = 5.1
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 9/68 (13%)
Query: 118 EDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFF-ISHEYSDY-SMIQNL 175
E T ++I LTFD + D + + +K TFF I E + S + +
Sbjct: 1 ETTEKVIALTFDDGPTPAHTDAILSILDEYD-------IKATFFLIGREIEENPSEARAI 53
Query: 176 ANRGHEIG 183
GHEIG
Sbjct: 54 VAAGHEIG 61
>gnl|CDD|173155 PRK14692, PRK14692, lagellar hook-associated protein FlgL;
Provisional.
Length = 749
Score = 29.2 bits (65), Expect = 5.3
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 12/82 (14%)
Query: 111 IPGGLDAEDTPQMILLTFDGAVNLNNYDHYQKVFSDSRKNPNGCPMKGTFFISHEYSDYS 170
I G A++ P + +G +N N+Y Q++ DS + T +S +Y
Sbjct: 524 IIGMFAADNIPTATIQANNGQINNNDYTQIQQLMKDS---------QATVDVSMDYKGRI 574
Query: 171 MIQNLANRGHEIGVETISLQDG 192
+ + + G I ISL D
Sbjct: 575 SVTDKLSSGTNIE---ISLSDS 593
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 29.0 bits (65), Expect = 5.5
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 315 DSDEVLEWLKEDFNKYYTQNKAPYMMPFHTNWFQIKELEQ 354
D+ EV WL++DF+K NK M + F I + E+
Sbjct: 556 DAIEVKSWLRKDFDKVLEINKLISKMEIFMDRFAIIKSEE 595
>gnl|CDD|237236 PRK12858, PRK12858, tagatose 1,6-diphosphate aldolase; Reviewed.
Length = 340
Score = 28.8 bits (65), Expect = 5.9
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 287 EVPLNAHFVESYEGGHCPYLDQCVLHNHDSDEVLEWLKE 325
EVP++ FVE ++G Y +E + +E
Sbjct: 206 EVPVDMKFVEGFDGFEEAY---------TQEEAFKLFRE 235
>gnl|CDD|182544 PRK10555, PRK10555, aminoglycoside/multidrug efflux system;
Provisional.
Length = 1037
Score = 29.0 bits (65), Expect = 6.3
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 323 LKEDFNKYYTQNKAPYMMPF----HTNW 346
L +D N +Y +NK M+PF + W
Sbjct: 780 LPDDINLWYVRNKDGGMVPFSAFATSRW 807
>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 = 27.9 bits (63), Expect = 7.3
Identities = 25/114 (21%), Positives = 37/114 (32%), Gaps = 40/114 (35%)
Query: 123 MILLTFDGAVNLNNYDH-------YQKVFSDSRKNPNGCPMKGTFFIS------------ 163
++LTFD +NY + Y + TFF+
Sbjct: 1 PVVLTFDDG-YRDNYTYALPILKKYG--------------LPATFFVITGYIGGGNPWWA 45
Query: 164 -----HEYSDYSMIQNLANRGHEIGVETISLQDGLQDKGYEEWVGEMIGMREIL 212
Y + ++ LA G EIG T + D L EE E+ +E L
Sbjct: 46 PAPPRPPYLTWDQLRELAASGVEIGSHTHTHPD-LTTLSDEELRRELAESKERL 98
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 0.137 0.453
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: 22,059,177
Number of extensions: 2064421
Number of successful extensions: 1607
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1586
Number of HSP's successfully gapped: 35
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
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: 60 (27.0 bits)