RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5813
(226 letters)
>gnl|CDD|119351 cd02872, GH18_chitolectin_chitotriosidase, This conserved domain
family includes a large number of catalytically inactive
chitinase-like lectins (chitolectins) including YKL-39,
YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic
mammalian chitinase), as well as catalytically active
chitotriosidases. The conserved domain is an
eight-stranded alpha/beta barrel fold belonging to the
family 18 glycosyl hydrolases. The fold has a
pronounced active-site cleft at the C-terminal end of
the beta-barrel. The chitolectins lack a key active
site glutamate (the proton donor required for hydrolytic
activity) but retain highly conserved residues involved
in oligosaccharide binding. Chitotriosidase is a
chitinolytic enzyme expressed in maturing macrophages,
which suggests that it plays a part in antimicrobial
defense. Chitotriosidase hydrolyzes chitotriose, as
well as colloidal chitin to yield chitobiose and is
therefore considered an exochitinase. Chitotriosidase
occurs in two major forms, the large form being
converted to the small form by either RNA or
post-translational processing. Although the small form,
containing the chitinase domain alone, is sufficient for
the chitinolytic activity, the additional C-terminal
chitin-binding domain of the large form plays a role in
processing colloidal chitin. The chitotriosidase gene is
nonessential in humans, as about 35% of the population
are heterozygous and 6% homozygous for an inactivated
form of the gene. HCGP39 is a 39-kDa human cartilage
glycoprotein thought to play a role in connective tissue
remodeling and defense against pathogens.
Length = 362
Score = 231 bits (592), Expect = 2e-75
Identities = 90/177 (50%), Positives = 119/177 (67%), Gaps = 7/177 (3%)
Query: 53 SYDIH---RYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYL 109
+YDI +YLDF+N+++YD+H ++E H+SPL+ D L++D+ IK++L
Sbjct: 170 AYDIPEISKYLDFINVMTYDFHGSWEGVTGHNSPLYAGSADTGDQ--KYLNVDYAIKYWL 227
Query: 110 KSGADPDKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLK 169
GA P+KLVLGIPTYGRS+TL +P + +GAPA GPG G TRE G+LAYYEIC LK
Sbjct: 228 SKGAPPEKLVLGIPTYGRSFTLASPSNTGVGAPASGPGTAGPYTREAGFLAYYEICEFLK 287
Query: 170 SDDWSVEHPNPRAMGPYAFKGNQWVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDNDD 226
S W+V + PYA+KGNQWVGYDD+E K +Y+ + LGG M WSID DD
Sbjct: 288 S-GWTVVW-DDEQKVPYAYKGNQWVGYDDEESIALKVQYLKSKGLGGAMVWSIDLDD 342
>gnl|CDD|214753 smart00636, Glyco_18, Glyco_18 domain.
Length = 334
Score = 179 bits (456), Expect = 2e-55
Identities = 71/173 (41%), Positives = 96/173 (55%), Gaps = 11/173 (6%)
Query: 55 DIHRYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGAD 114
I +YLDF+N+++YD+H A+ H++PL+ D E ++D+ +K+YL G
Sbjct: 171 AIAKYLDFINLMTYDFHGAWSNPTGHNAPLYAGPGDPEK-----YNVDYAVKYYLCKGVP 225
Query: 115 PDKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLKSDDWS 174
P KLVLGIP YGR +TL + +N GAP GP G T E G + Y EIC L +
Sbjct: 226 PSKLVLGIPFYGRGWTLVDGSNNGPGAPFTGPATGGPGTWEGGVVDYREICKLLGAT--- 282
Query: 175 VEHPNPRAMGPYAFKGN--QWVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDND 225
+ A PYA+ QWV YDD K KA YV D+ LGG+M W +D D
Sbjct: 283 -VVYDDTAKAPYAYNPGTGQWVSYDDPRSIKAKADYVKDKGLGGVMIWELDAD 334
>gnl|CDD|216071 pfam00704, Glyco_hydro_18, Glycosyl hydrolases family 18.
Length = 325
Score = 149 bits (377), Expect = 8e-44
Identities = 73/171 (42%), Positives = 101/171 (59%), Gaps = 17/171 (9%)
Query: 55 DIHRYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGAD 114
I +YLDF+N+++YD+H + ++PL+ + ++D+ +++YLK+G
Sbjct: 172 KIGKYLDFINLMTYDFHG-WSNITGPNAPLY---------DGSWQNVDYAVQYYLKAGVP 221
Query: 115 PDKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLKSDDWS 174
KLVLGIP YGR +TL N N GAPA GPG T E G L+Y EIC+ LKS
Sbjct: 222 ASKLVLGIPFYGRGWTLVNGSGNGGGAPAPGPG-----TWEGGILSYKEICALLKSG-AG 275
Query: 175 VEHPNPRAMGPYAFKGNQWVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDND 225
+ + A PY +KG Q+V YDD K KAKYV D+ LGG+M WS+D D
Sbjct: 276 PGYDDT-AKAPYIYKGKQFVSYDDPRSIKAKAKYVKDKGLGGVMIWSLDQD 325
Score = 37.9 bits (88), Expect = 0.002
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 3 VKKKNTYLDFMNILSYDYHSAFEPAVNHHSPLF 35
+ K YLDF+N+++YD+H + ++PL+
Sbjct: 170 IAKIGKYLDFINLMTYDFHG-WSNITGPNAPLY 201
>gnl|CDD|119365 cd06548, GH18_chitinase, The GH18 (glycosyl hydrolases, family 18)
type II chitinases hydrolyze chitin, an abundant polymer
of N-acetylglucosamine and have been identified in
bacteria, fungi, insects, plants, viruses, and protozoan
parasites. The structure of this domain is an
eight-stranded alpha/beta barrel with a pronounced
active-site cleft at the C-terminal end of the
beta-barrel.
Length = 322
Score = 117 bits (295), Expect = 1e-31
Identities = 53/172 (30%), Positives = 78/172 (45%), Gaps = 48/172 (27%)
Query: 56 IHRYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGADP 115
I +YLDF+N+++YD+H A+ HHS L+ D + S+D + +YL +G P
Sbjct: 197 IAKYLDFINLMTYDFHGAWSNTTGHHSNLYASPADPPGGY----SVDAAVNYYLSAGVPP 252
Query: 116 DKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLKSDDWSV 175
+KLVLG+P YGR +T GY Y+
Sbjct: 253 EKLVLGVPFYGRGWT--------------------------GYTRYW------------- 273
Query: 176 EHPNPRAMGPYAFKGN--QWVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDND 225
+ A PY + + ++ YDD K KA YV D+ LGG+MFW + D
Sbjct: 274 ---DEVAKAPYLYNPSTKTFISYDDPRSIKAKADYVKDKGLGGVMFWELSGD 322
>gnl|CDD|119352 cd02873, GH18_IDGF, The IDGF's (imaginal disc growth factors) are a
family of growth factors identified in insects that
include at least five members, some of which are encoded
by genes in a tight cluster. The IDGF's have an
eight-stranded alpha/beta barrel fold and are related to
the glycosyl hydrolase family 18 (GH18) chitinases, but
they have an amino acid substitution known to abolish
chitinase catalytic activity. IDGFs may have evolved
from chitinases to gain new functions as growth factors,
interacting with cell surface glycoproteins involved in
growth-promoting processes.
Length = 413
Score = 110 bits (276), Expect = 3e-28
Identities = 60/194 (30%), Positives = 93/194 (47%), Gaps = 31/194 (15%)
Query: 56 IHRYLDFMNILSYDYHS-AFEPAVNHHS-PL-FPLEEDGEYNFEAQLSIDHTIKHYLKSG 112
I +DF+N+ ++D+ + P ++ P+ E + +N +D+ +K++L G
Sbjct: 208 IANNVDFVNLATFDFLTPERNPEEADYTAPIYELYERNPHHN------VDYQVKYWLNQG 261
Query: 113 ADPDKLVLGIPTYGRSYTLFNPESNQIGAP----ADGPGEQGDATREKGYLAYYEICS-- 166
KL LGI TYGR++ L +S G P DGPG G T+ G L++ EICS
Sbjct: 262 TPASKLNLGIATYGRAWKL-TKDSGITGVPPVLETDGPGPAGPQTKTPGLLSWPEICSKL 320
Query: 167 ----SLKSDDW---SVEHPNPRAMGPYAFKGNQ-------WVGYDDQEIAKDKAKYVNDQ 212
+LK D V P R G YA++ WV Y+D + A +KA Y +
Sbjct: 321 PNPANLKGADAPLRKVGDPTKR-FGSYAYRPADENGEHGIWVSYEDPDTAANKAGYAKAK 379
Query: 213 KLGGIMFWSIDNDD 226
LGG+ + + DD
Sbjct: 380 GLGGVALFDLSLDD 393
>gnl|CDD|119358 cd02879, GH18_plant_chitinase_class_V, The class V plant chitinases
have a glycosyl hydrolase family 18 (GH18) domain, but
lack the chitin-binding domain present in other GH18
enzymes. The GH18 domain of the class V chitinases has
endochitinase activity in some cases and no catalytic
activity in others. Included in this family is a lectin
found in black locust (Robinia pseudoacacia) bark, which
binds chitin but lacks chitinase activity. Also
included is a chitinase-related receptor-like kinase
(CHRK1) from tobacco (Nicotiana tabacum), with an
N-terminal GH18 domain and a C-terminal kinase domain,
which is thought to be part of a plant signaling
pathway. The GH18 domain of CHRK1 is expressed
extracellularly where it binds chitin but lacks
chitinase activity.
Length = 299
Score = 94.7 bits (236), Expect = 2e-23
Identities = 47/200 (23%), Positives = 78/200 (39%), Gaps = 61/200 (30%)
Query: 27 AVNHHSPLFPLEEDGEYNFEAQLSIVSYDIHRYLDFMNILSYDYHSAFEPAVNHHSPLFP 86
AV LF ++ Y EA I++ LD++N+++YDY+ ++E +
Sbjct: 156 AVYFSPILFLSDDSVSYPIEA--------INKNLDWVNVMAYDYYGSWESNTTGPAAALY 207
Query: 87 LEEDGEYNFEAQLSIDHTIKHYLKSGADPDKLVLGIPTYGRSYTLFNPESNQIGAPADGP 146
+S D+ IK ++K+G KLVLG+P YGR++TL++ +
Sbjct: 208 DPNSN-------VSTDYGIKSWIKAGVPAKKLVLGLPLYGRAWTLYDTTT---------- 250
Query: 147 GEQGDATREKGYLAYYEICSSLKSDDWSVEHPNPRAMGPYAFKGNQWVGYDDQEIAKDKA 206
+ Y + G W+GYDD + K
Sbjct: 251 ------------------------------------VSSYVYAGTTWIGYDDVQSIAVKV 274
Query: 207 KYVNDQKLGGIMFWSIDNDD 226
KY + L G W++ DD
Sbjct: 275 KYAKQKGLLGYFAWAVGYDD 294
Score = 32.3 bits (74), Expect = 0.14
Identities = 8/30 (26%), Positives = 17/30 (56%)
Query: 7 NTYLDFMNILSYDYHSAFEPAVNHHSPLFP 36
N LD++N+++YDY+ ++E +
Sbjct: 178 NKNLDWVNVMAYDYYGSWESNTTGPAAALY 207
>gnl|CDD|225862 COG3325, ChiA, Chitinase [Carbohydrate transport and metabolism].
Length = 441
Score = 96.0 bits (239), Expect = 4e-23
Identities = 50/186 (26%), Positives = 84/186 (45%), Gaps = 15/186 (8%)
Query: 55 DIHRYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEY---NFEAQLSIDHT--IKHYL 109
+I +Y+D++NI++YD+H A+ + HH+ L+ +D F +D ++
Sbjct: 238 EIAQYVDYINIMTYDFHGAWNETLGHHAALYGTPKDPPLANGGFYVDAEVDGIDWLEEGF 297
Query: 110 KSGADPDKLVLGIPTYGRSYTLFNPESN--------QIGAPADGPGEQGDATREKGYLAY 161
P KLVLG+P YGR + + S + G +K Y
Sbjct: 298 AGDVPPSKLVLGMPFYGRGWNGVDGGSLGTCPGLYQGLDNSGIPKGTWEAGNGDKDYGKA 357
Query: 162 YEICSSLKSDDWSVEHPNPRAMGPYAF--KGNQWVGYDDQEIAKDKAKYVNDQKLGGIMF 219
Y++ ++ + + + A PY + + ++ YDD K KA+YV D LGG+MF
Sbjct: 358 YDLDANNAGKNGYERYWDDVAKAPYLYNPEKGVFISYDDPRSVKAKAEYVADNNLGGMMF 417
Query: 220 WSIDND 225
W I D
Sbjct: 418 WEISGD 423
>gnl|CDD|119357 cd02878, GH18_zymocin_alpha, Zymocin, alpha subunit. Zymocin is a
heterotrimeric enzyme that inhibits yeast cell cycle
progression. The zymocin alpha subunit has a chitinase
activity that is essential for holoenzyme action from
the cell exterior while the gamma subunit contains the
intracellular toxin responsible for G1 phase cell cycle
arrest. The zymocin alpha and beta subunits are thought
to act from the cell's exterior by docking to the cell
wall-associated chitin, thus mediating gamma-toxin
translocation. The alpha subunit has an eight-stranded
TIM barrel fold similar to that of family 18 glycosyl
hydrolases such as hevamine, chitolectin, and
chitobiase.
Length = 345
Score = 55.4 bits (134), Expect = 3e-09
Identities = 41/177 (23%), Positives = 74/177 (41%), Gaps = 11/177 (6%)
Query: 54 YDIHRYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHT---IKHYLK 110
D+ +Y+D++ ++YD H ++ SP P G + ++ T + K
Sbjct: 171 KDMAKYVDYIVYMTYDLHGQWDYGNKWASPGCP---AGNC-LRSHVNKTETLDALSMITK 226
Query: 111 SGADPDKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREK---GYLAYYEICSS 167
+G +K+V+G+ +YGRS+ + +P G GPG +A R GY A EI
Sbjct: 227 AGVPSNKVVVGVASYGRSFKMADPGCTGPGCTFTGPGSGAEAGRCTCTAGYGAISEIEII 286
Query: 168 LKSDDWSVEHPNPRAMGPYA-FKGNQWVGYDDQEIAKDKAKYVNDQKLGGIMFWSID 223
S + + + + +QWV Y + ++ GG W++D
Sbjct: 287 DISKSKNKRWYDTDSDSDILVYDDDQWVAYMSPATKAARIEWYKGLNFGGTSDWAVD 343
>gnl|CDD|119354 cd02875, GH18_chitobiase, Chitobiase (also known as
di-N-acetylchitobiase) is a lysosomal glycosidase that
hydrolyzes the reducing-end N-acetylglucosamine from the
chitobiose core of oligosaccharides during the ordered
degradation of asparagine-linked glycoproteins in
eukaryotes. Chitobiase can only do so if the asparagine
that joins the oligosaccharide to protein is previously
removed by a glycosylasparaginase. Chitobiase is
therefore the final step in the lysosomal degradation of
the protein/carbohydrate linkage component of
asparagine-linked glycoproteins. The catalytic domain of
chitobiase is an eight-stranded alpha/beta barrel fold
similar to that of other family 18 glycosyl hydrolases
such as hevamine and chitotriosidase.
Length = 358
Score = 46.3 bits (110), Expect = 5e-06
Identities = 48/190 (25%), Positives = 66/190 (34%), Gaps = 43/190 (22%)
Query: 56 IHRYLDFMNILSYDYHS---AFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSG 112
I DF+ ++ YD S E +SP + G ++ K G
Sbjct: 175 IADASDFLVVMDYDEQSQIWGKECIAGANSP-YSQTLSG-------------YNNFTKLG 220
Query: 113 ADPDKLVLGIPTYGRSYTLFN----------PESNQIGAP-ADGPGEQGDATREKGYLAY 161
DP KLV+G+P YG Y N P+ GA +D G Q + Y
Sbjct: 221 IDPKKLVMGLPWYGYDYPCLNGNLEDVVCTIPKVPFRGANCSDAAGRQ---------IPY 271
Query: 162 YEICSSLKSDD----WSVEHPNPRAMGPYAFKGNQ-WVGYDDQEIAKDKAKYVNDQKLGG 216
EI + S W E +GN V YD+ + K Y + L G
Sbjct: 272 SEIMKQINSSIGGRLWDSEQ-KSPFYNYKDKQGNLHQVWYDNPQSLSIKVAYAKNLGLKG 330
Query: 217 IMFWSIDNDD 226
I W+ D D
Sbjct: 331 IGMWNGDLLD 340
>gnl|CDD|119353 cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic enzyme
(CFLE) is a peptidoglycan hydrolase involved in
bacterial endospore germination. CFLE is expressed as
an inactive preprotein (called SleB) in the forespore
compartment of sporulating cells. SleB translocates
across the forespore inner membrane and is deposited as
a mature enzyme in the cortex layer of the spore. As
part of a sensory mechanism capable of initiating
germination, CFLE degrades a spore-specific
peptidoglycan constituent called muramic-acid
delta-lactam that comprises the outer cortex. CFLE has
a C-terminal glycosyl hydrolase family 18 (GH18)
catalytic domain as well as two N-terminal LysM
peptidoglycan-binding domains. In addition to SleB,
this family includes YaaH, YdhD, and YvbX from Bacillus
subtilis.
Length = 313
Score = 40.7 bits (96), Expect = 3e-04
Identities = 37/178 (20%), Positives = 69/178 (38%), Gaps = 38/178 (21%)
Query: 54 YDIH-RYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSG 112
Y + +DF+ +++YD+H P P+ P+ ++ ++ Y +
Sbjct: 162 YAAIGKIVDFVVLMTYDWHWRGGP----PGPVAPIGW-----------VERVLQ-YAVTQ 205
Query: 113 ADPDKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLKSDD 172
+K++LGIP YG +TL + G A Q K Y A EI
Sbjct: 206 IPREKILLGIPLYGYDWTL----PYKKGGKASTISPQQAINLAKRYGA--EI-------Q 252
Query: 173 WSVEHPNPRAMGPYAFKGNQ----WVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDNDD 226
+ E +P + + Q V ++D + K + + L G+ +W + +D
Sbjct: 253 YDEEAQSP----FFRYVDEQGRRHEVWFEDARSLQAKFELAKEYGLRGVSYWRLGLED 306
>gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family
18) type II chitinases hydrolyze chitin, an abundant
polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc)
which is a major component of the cell wall of fungi and
the exoskeleton of arthropods. Chitinases have been
identified in viruses, bacteria, fungi, protozoan
parasites, insects, and plants. The structure of the
GH18 domain is an eight-stranded beta/alpha barrel with
a pronounced active-site cleft at the C-terminal end of
the beta-barrel. The GH18 family includes
chitotriosidase, chitobiase, hevamine, zymocin-alpha,
narbonin, SI-CLP (stabilin-1 interacting chitinase-like
protein), IDGF (imaginal disc growth factor), CFLE
(cortical fragment-lytic enzyme) spore hydrolase, the
type III and type V plant chitinases, the
endo-beta-N-acetylglucosaminidases, and the
chitolectins. The GH85 (glycosyl hydrolase, family 85)
ENGases (endo-beta-N-acetylglucosaminidases) are closely
related to the GH18 chitinases and are included in this
alignment model.
Length = 210
Score = 36.2 bits (84), Expect = 0.006
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 203 KDKAKYVNDQKLGGIMFWSIDND 225
KAKY + LGG+M W +D D
Sbjct: 188 GAKAKYAKQKGLGGVMIWELDQD 210
>gnl|CDD|119362 cd06545, GH18_3CO4_chitinase, The Bacteroides thetaiotaomicron
protein represented by pdb structure 3CO4 is an
uncharacterized bacterial member of the family 18
glycosyl hydrolases with homologs found in
Flavobacterium, Stigmatella, and Pseudomonas.
Length = 253
Score = 35.9 bits (83), Expect = 0.009
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 18/76 (23%)
Query: 58 RYLDFMNILSYDYHSAFEPAVN--HHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGADP 115
Y DF+NI+SYD + N HS Y+ A ++ ++ + G
Sbjct: 153 AYFDFINIMSYD-ATGPWWGDNPGQHSS---------YDD-AVNDLN----YWNERGLAS 197
Query: 116 -DKLVLGIPTYGRSYT 130
DKLVLG+P YG +
Sbjct: 198 KDKLVLGLPFYGYGFY 213
>gnl|CDD|226376 COG3858, COG3858, Predicted glycosyl hydrolase [General function
prediction only].
Length = 423
Score = 32.8 bits (75), Expect = 0.12
Identities = 30/169 (17%), Positives = 62/169 (36%), Gaps = 28/169 (16%)
Query: 58 RYLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGADPDK 117
+ DF+ +++YD+H + P P+ + + I++ L +K
Sbjct: 271 KIADFVILMTYDWHYSGGP----PGPVASIGW-----------VRKVIEYALTV-IPAEK 314
Query: 118 LVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDATREKGYLAYYEICSSLKSDDWSVEH 177
+++GIP YG +TL +G A Y A + ++ +S +
Sbjct: 315 VMMGIPLYGYDWTLPYDP---LGYLARAISPDEAIDIANRYNATIQYDATSQSPFFYYVD 371
Query: 178 PNPRAMGPYAFKGNQWVGYDDQEIAKDKAKYVNDQKLGGIMFWSIDNDD 226
R V ++D + K + + L G+ +W + +D
Sbjct: 372 KEGR---------YHEVWFEDARSFQTKLDLIKEYGLRGVSYWVLGQED 411
>gnl|CDD|235558 PRK05683, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 676
Score = 29.7 bits (67), Expect = 1.3
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 115 PDKLVLGIPTYG-RSYTLFNPESNQIGAPADGPGE 148
P KLV G + G +SYTL + + N IG+ PG+
Sbjct: 486 PVKLVFGADSSGPQSYTLVDAKGNAIGSGTIVPGQ 520
>gnl|CDD|165517 PHA03259, PHA03259, Capsid triplex subunit 2; Provisional.
Length = 302
Score = 29.3 bits (66), Expect = 1.4
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 8/37 (21%)
Query: 116 DKLVLGIPTYGRSYTLFNPESNQIGAPADGPGEQGDA 152
++L+LG+PT+G YT+ N P E+GD
Sbjct: 76 NQLLLGVPTHGHLYTIKNT------GPV--LWEKGDT 104
>gnl|CDD|233425 TIGR01467, cobI_cbiL, precorrin-2 C20-methyltransferase. This
model represents precorrin-2 C20-methyltransferase, one
of several closely related
S-adenosylmethionine-dependent methyltransferases
involved in cobalamin (vitamin B12) biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 230
Score = 28.8 bits (65), Expect = 2.1
Identities = 11/54 (20%), Positives = 19/54 (35%)
Query: 71 HSAFEPAVNHHSPLFPLEEDGEYNFEAQLSIDHTIKHYLKSGADPDKLVLGIPT 124
+FP+ +D + +A + L+ G D L LG P+
Sbjct: 49 DYLKPNDTRILELVFPMTKDRDELEKAWDEAAEAVAAELEEGRDVAFLTLGDPS 102
>gnl|CDD|213962 TIGR04349, rSAM_QueE_gams, putative 7-cyano-7-deazaguanosine
(preQ0) biosynthesis protein QueE, gammaproteobacterial
type. Members of this radical SAM domain protein family
appear to be a form of the queuosine biosynthesis
protein QueE. QueE is involved in making preQ0
(7-cyano-7-deazaquanine), a precursor of both the
bacterial/eukaryotic modified tRNA base queuosine and
the archaeal modified base archaeosine. Members occur in
preQ0 operons species that lack members of related
protein family TIGR03365.
Length = 210
Score = 27.2 bits (61), Expect = 5.5
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 186 YAFKGNQWVGYDD--QEIAKDKAKYV 209
YAF G + + DD ++A A+YV
Sbjct: 40 YAFSGGERMSLDDILAQVASYGARYV 65
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP
dependent enzyme and catalyzes the committed step of
methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 27.2 bits (61), Expect = 7.0
Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 8/68 (11%)
Query: 101 IDHTIKHYLKSGADPDKLVLGIPTYGRSYTLFNPESNQIG-----APADGPGEQGDATRE 155
I + LK+G D +V YG +Y LF ++G D P A +
Sbjct: 68 ISTVLLALLKAG---DHVVASDDLYGGTYRLFERLLPKLGIEVTFVDPDDPEALEAAIKP 124
Query: 156 KGYLAYYE 163
+ L Y E
Sbjct: 125 ETKLVYVE 132
>gnl|CDD|237725 PRK14487, PRK14487, cbb3-type cytochrome c oxidase subunit II;
Provisional.
Length = 217
Score = 27.1 bits (61), Expect = 7.3
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 24/63 (38%)
Query: 170 SDDWSVEH-PNPRA------MGPYAF---------------KGNQWVG--YDDQEIAKDK 205
SD+W H NPR+ M Y + + VG Y D++IA K
Sbjct: 115 SDEWHRNHLINPRSVVPESNMPAYPWLAENDLDGTDTAEKMTALRVVGVPYTDEDIAGAK 174
Query: 206 AKY 208
A
Sbjct: 175 AAV 177
>gnl|CDD|220014 pfam08780, NTase_sub_bind, Nucleotidyltransferase substrate binding
protein like. Nucleotidyltransferases (EC 2.7.7)
comprise a large enzyme family with diverse roles in
polynucleotide synthesis and modification. This domain
is structurally related to kanamycin
nucleotidyltransferase (KNTase) and forms a complex with
HI0073, a sequence homolog of the nucleotide-binding
domain of this nucleotidyltransferase superfamily.
Length = 122
Score = 26.0 bits (58), Expect = 8.5
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 72 SAFEPAVNHHSPLFPLEEDG-----EYNFEAQLSIDHTIKHYLKSGADPD 116
++ E A+ PL LE DG E+ +E L+ +K YL+ D
Sbjct: 11 ASLEEALELSDPLNDLERDGVIQRFEFTYE--LAWK-LLKDYLEYQGIVD 57
>gnl|CDD|119355 cd02876, GH18_SI-CLP, Stabilin-1 interacting chitinase-like protein
(SI-CLP) is a eukaryotic chitinase-like protein of
unknown function that interacts with the
endocytic/sorting transmembrane receptor stabilin-1 and
is secreted from the lysosome. SI-CLP has a glycosyl
hydrolase family 18 (GH18) domain but lacks a
chitin-binding domain. The catalytic amino acids of the
GH18 domain are not conserved in SI-CLP, similar to the
chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is
sorted to late endosomes and secretory lysosomes in
alternatively activated macrophages.
Length = 318
Score = 26.9 bits (60), Expect = 9.8
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 19/75 (25%)
Query: 59 YLDFMNILSYDYHSAFEPAVNHHSPLFPLEEDGEYNFEAQLS-IDHTIKHYLK-SGADPD 116
++D ++++YDY S P N A LS + ++ L SG
Sbjct: 178 HVDGFSLMTYDYSSPQRPGPN-----------------APLSWVRSCLELLLPESGKKRA 220
Query: 117 KLVLGIPTYGRSYTL 131
K++LG+ YG YTL
Sbjct: 221 KILLGLNFYGNDYTL 235
>gnl|CDD|111339 pfam02433, FixO, Cytochrome C oxidase, mono-heme subunit/FixO. The
bacterial oxidase complex, fixNOPQ or cytochrome cbb3,
is thought to be required for respiration in
endosymbiosis. FixO is a membrane bound mono-heme
constituent of the fixNOPQ complex.
Length = 226
Score = 26.8 bits (60), Expect = 9.9
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 24/61 (39%)
Query: 170 SDDWSVEH-PNPRA------MGPYAF---------------KGNQWVG--YDDQEIAKDK 205
SDDW V H +PR+ M YA+ K + VG Y D+ I K
Sbjct: 114 SDDWHVAHLRDPRSVVPESIMPAYAWLAENPLDTSDIADKLKALRTVGVPYTDEMIENAK 173
Query: 206 A 206
A
Sbjct: 174 A 174
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.136 0.421
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,015,018
Number of extensions: 1132746
Number of successful extensions: 815
Number of sequences better than 10.0: 1
Number of HSP's gapped: 794
Number of HSP's successfully gapped: 37
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 57 (25.8 bits)