RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17999
(335 letters)
>gnl|CDD|217370 pfam03102, NeuB, NeuB family. NeuB is the prokaryotic
N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes
the direct formation of Neu5Ac (the most common sialic
acid) by condensation of phosphoenolpyruvate (PEP) and
N-acetylmannosamine (ManNAc). This reaction has only
been observed in prokaryotes; eukaryotes synthesise the
9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P
instead of ManNAc. Such eukaryotic enzymes are not
present in this family. This family also contains SpsE
spore coat polysaccharide biosynthesis proteins.
Length = 240
Score = 295 bits (758), Expect = e-100
Identities = 94/259 (36%), Positives = 141/259 (54%), Gaps = 25/259 (9%)
Query: 1 ECGADCVKFQKSCLSTKFTQSALDRPYLSPHAW-ANTYGQHKQHLEFSQEEYVMLQQCAD 59
E GAD VKFQ T +++A Y + W + + + LE +E + L +
Sbjct: 6 EAGADAVKFQTFTADTLVSKNADKADYQIGNLWGGESQYELLKKLELPEEWHKELFEYCK 65
Query: 60 QVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLIISTGMLPSI 119
+ I F ++ D S DFL S VP KI SG+ N+PL++Y A KP+I+STGM ++
Sbjct: 66 EKGIEFFSTPFDLESVDFLESLGVPAYKIASGEITNLPLLRYIAKTGKPVILSTGM-ATL 124
Query: 120 EHVDNIYTTVKQYHSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSAYPTPYHDINLNV 179
E ++ T+++ + ++++LHC S YP P+ D+NL
Sbjct: 125 EEIEEAVETLREAGNE----------------------DITLLHCTSEYPAPFEDVNLRA 162
Query: 180 IHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQIIEKHFTLDKSWKGSDHASSLTPPEL 239
I TL+ + +P+GYS H G+ AAVA+GA +IEKHFTLD++ G DH +SL P EL
Sbjct: 163 IPTLKEAFG-VPVGYSDHTLGIEAPIAAVALGASVIEKHFTLDRNLPGPDHKASLEPDEL 221
Query: 240 KALVTGIRDIEQSLGSPTK 258
K LV IR++E++LG K
Sbjct: 222 KELVKDIRNVEKALGDGVK 240
>gnl|CDD|234264 TIGR03569, NeuB_NnaB, N-acetylneuraminate synthase. This family is
a subset of the pfam03102 and is believed to include
only authentic NeuB N-acetylneuraminate (sialic acid)
synthase enzymes. The majority of the genes identified
by this model are observed adjacent to both the NeuA and
NeuC genes which together effect the biosynthesis of
CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Length = 329
Score = 274 bits (702), Expect = 8e-91
Identities = 125/336 (37%), Positives = 175/336 (52%), Gaps = 44/336 (13%)
Query: 1 ECGADCVKFQ--KSC-LSTKFTQSALDRPYLSPHAWANTYGQHKQH-----LEFSQEEYV 52
E GAD VKFQ K+ L +K A + NT + Q LE S+E++
Sbjct: 27 EAGADAVKFQTFKAEDLVSKNAPKA-------EYQKINTGAEESQLEMLKKLELSEEDHR 79
Query: 53 MLQQCADQVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLIIS 112
L++ + I F ++ D S DFL VP KI SG+ N PL+K A KP+I+S
Sbjct: 80 ELKEYCESKGIEFLSTPFDLESADFLEDLGVPRFKIPSGEITNAPLLKKIARFGKPVILS 139
Query: 113 TGM--LPSIEHVDNIYTTVKQYHSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSAYPT 170
TGM L IE + +L A SN+++LHC + YP
Sbjct: 140 TGMATLEEIEAA-------------VGVL--RDAGTP--------DSNITLLHCTTEYPA 176
Query: 171 PYHDINLNVIHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQIIEKHFTLDKSWKGSDH 230
P+ D+NLN + TL+ + D+P+GYS H G+ AAVA+GA +IEKHFTLDK+ G DH
Sbjct: 177 PFEDVNLNAMDTLKEAF-DLPVGYSDHTLGIEAPIAAVALGATVIEKHFTLDKNLPGPDH 235
Query: 231 ASSLTPPELKALVTGIRDIEQSLGSPTKRMQVSEAPCYAKLGKCIVSSCDIQAGTVLQEF 290
+SL P ELK +V GIR++E++LG KR SE K +V++ DI+ G + E
Sbjct: 236 KASLEPDELKEMVQGIRNVEKALGDGVKRPTPSEQKNRDVARKSLVAAKDIKKGEIFTED 295
Query: 291 HVCIKVAEP-KGICGTRYASVMGRKVNRDIRRDESI 325
++ +K P GI Y V+G+K +RD DE I
Sbjct: 296 NLTVK--RPGNGISPMEYWEVIGKKASRDYEEDELI 329
>gnl|CDD|225000 COG2089, SpsE, Sialic acid synthase [Cell envelope biogenesis,
outer membrane].
Length = 347
Score = 261 bits (668), Expect = 2e-85
Identities = 111/327 (33%), Positives = 169/327 (51%), Gaps = 28/327 (8%)
Query: 1 ECGADCVKFQKSCLSTKFTQSALDRPYLSPHAWAN-TYGQHKQHLEFSQEEYVMLQQCAD 59
E GAD VKFQ T + + P+ W + + + E E + L++ A
Sbjct: 41 EAGADAVKFQTFYTPDIMTLESKNVPFKIKTLWDKVSLYELYEEAETPLEWHAQLKEYAR 100
Query: 60 QVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLIISTGMLPSI 119
+ I+F +S D + D L S N P KI SG+ N++PLIKY A K KP+I+STGM +I
Sbjct: 101 KRGIIFFSSPFDLTAVDLLESLNPPAYKIASGEINDLPLIKYIAKKGKPIILSTGM-ATI 159
Query: 120 EHVDNIYTTVKQYHSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSAYPTPYHDINLNV 179
E ++ +++ + ++++LHC SAYP P+ D+NL
Sbjct: 160 EEIEEAVAILRENGNP----------------------DIALLHCTSAYPAPFEDVNLKA 197
Query: 180 IHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQIIEKHFTLDKSWKGSDHASSLTPPEL 239
I L + + +G S H G+ AAVA+GA +IEKHFTLDKS +G DHA SL P E
Sbjct: 198 IPKLAEAF-NAIVGLSDHTLGILAPLAAVALGASVIEKHFTLDKSREGPDHAFSLDPDEF 256
Query: 240 KALVTGIRDIEQSLGSPTKRMQVSEAPCYAKLGKCIVSSCDIQAGTVLQEFHVCIKVAEP 299
K +V IR +E++LG K + SE + +V++ DI+ G +L E + +KV P
Sbjct: 257 KEMVDAIRQVEKALGDGEKEILPSEEETRNFARRSLVATKDIKKGEILSEDN--LKVLRP 314
Query: 300 -KGICGTRYASVMGRKVNRDIRRDESI 325
G+ Y ++G+K +DI+ +
Sbjct: 315 GNGLHPKEYEELLGKKATKDIKAGTPL 341
>gnl|CDD|163337 TIGR03586, PseI, pseudaminic acid synthase. Members of this family
are included within the larger pfam03102 (NeuB) family.
NeuB itself (TIGR03569) is involved in the biosynthesis
of neuraminic acid by the condensation of
phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine.
In an analagous reaction, this enzyme, PseI , condenses
PEP with 6-deoxy-beta-L-AltNAc4NAc to generate
pseudaminic acid.
Length = 327
Score = 166 bits (423), Expect = 4e-49
Identities = 101/330 (30%), Positives = 151/330 (45%), Gaps = 43/330 (13%)
Query: 1 ECGADCVKFQKSCLSTKFTQSALDRPYLSPH--AWANT-----YGQHKQHLEFSQEEYVM 53
GAD +K Q T S DRP W Y + E+ +E
Sbjct: 28 AAGADAIKLQTYTPDTITLDS--DRPEFIIKGGLWDGRTLYDLYQEAHTPWEWHKE---- 81
Query: 54 LQQCADQVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLIIST 113
L + A ++ + +S D+ + DFL S +VP KI S + ++PLI+Y A KP+I+ST
Sbjct: 82 LFERAKELGLTIFSSPFDETAVDFLESLDVPAYKIASFEITDLPLIRYVAKTGKPIIMST 141
Query: 114 GMLPSIEHVDNIYTTVKQYHSNLSILHCVSAYPTPYPTVKQY-HSNLSILHCVSAYPTPY 172
G+ E I V+ ++ +L +L C S+YP P
Sbjct: 142 GIATLEE----IQEAVE--------------------ACREAGCKDLVLLKCTSSYPAPL 177
Query: 173 HDINLNVIHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQIIEKHFTLDKSWKGSDHAS 232
D NL I L R+ ++P+G S H G+ AAVA+GA +IEKHFTLD+S G D A
Sbjct: 178 EDANLRTIPDLAERF-NVPVGLSDHTLGILAPVAAVALGACVIEKHFTLDRSDGGVDSAF 236
Query: 233 SLTPPELKALVTGIRDIEQSLGSPTKRMQVSEAPCYAKLGKCIVSSCDIQAGTVLQEFHV 292
SL P E KALV +R+ +LG + E + + + DI+ G E +V
Sbjct: 237 SLEPDEFKALVKEVRNAWLALGEVNYELSEKEKKS-RQFRRSLYVVKDIKKGETFTEENV 295
Query: 293 CIKVAEP-KGICGTRYASVMGRKVNRDIRR 321
+ P G+ ++G+K N+DI++
Sbjct: 296 --RSVRPGFGLHPKYLDEILGKKANQDIKK 323
>gnl|CDD|212160 cd11615, SAF_NeuB_like, C-terminal SAF domain of sialic acid
synthetase. Sialic acid synthetase (N-acetylneuraminate
synthase or N-acetylneuraminate-9-phosphate synthase)
catalyzes the condensation of phosphoenolpyruvate with
N-acetylmannosamine (ManNAc, in bacteria) or
N-acetylmannosamine-6-phosphate (ManNAc-6P, in mammals),
to yield N-acetylneuramic acid (NeuNAc) or
N-acetylneuramic acid-9-phosphate (NeuNAc-9P),
respectively. The N-terminal NeuB domain, a
TIM-barrel-like structure, contains the catalytic site,
the function of the SAF domain is not as clear. It may
participate in domain-swapped dimerization and play a
role in binding the substrate, in either domain-swapped
dimers or by directly interacting with the N-terminal
domain. Also included in the family are PEP-sugar
pyruvyltransferases known as spore coat polysaccharide
biosynthesis proteins (SpsE).
Length = 58
Score = 51.6 bits (125), Expect = 4e-09
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 272 GKCIVSSCDIQAGTVLQEFHVCIKVAEPKGICGTRYASVMGRKVNRDIRRDESIQDIDL 330
+ +V++ DI+AG VL E ++ +K G+ V+G+K RDI+ E + DL
Sbjct: 1 RRSLVAARDIKAGEVLTEENLRVKRPG-GGLSPKYLDEVLGKKAKRDIKAGEPLTWDDL 58
>gnl|CDD|219961 pfam08666, SAF, SAF domain. This domain family includes a range of
different proteins. Such as antifreeze proteins and
flagellar FlgA proteins, and CpaB pilus proteins.
Length = 63
Score = 39.5 bits (93), Expect = 1e-04
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 272 GKCIVSSCDIQAGTVLQEFHVCIK---VAEPKGICGTRYASVMGRKVNRDIRRDESI 325
+V++ D+ AG VL + + + P G+ Y V+G+ RDI E +
Sbjct: 1 DNVVVAARDLPAGEVLTADDLTLVRPPLDLPAGLAADAYGEVIGKVAKRDIAAGEPL 57
>gnl|CDD|181535 PRK08673, PRK08673, 3-deoxy-7-phosphoheptulonate synthase;
Reviewed.
Length = 335
Score = 41.4 bits (98), Expect = 4e-04
Identities = 22/53 (41%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 204 CYAAVAMGAQ--IIEKHFTLDKSWKGSDHASSLTPPELKALVTGIRDIEQSLG 254
AAVA GA I+E H +K+ SD SLTP E + L+ +R I ++LG
Sbjct: 283 ALAAVAAGADGLIVEVHPDPEKAL--SDGPQSLTPEEFEELMKKLRAIAEALG 333
>gnl|CDD|214862 smart00858, SAF, This domain family includes a range of different
proteins. Such as antifreeze proteins and flagellar FlgA
proteins, and CpaB pilus proteins.
Length = 63
Score = 35.2 bits (82), Expect = 0.003
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 275 IVSSCDIQAGTVLQE-----FHVCIKVAEPKGICGTRYASVMGRKVNRDIRRDE 323
+V++ D+ AG V+ HV ++ G+ T Y V+GR RDI E
Sbjct: 4 VVAARDLPAGEVITAEDLRLGHVALRDLPGGGL--TPYGQVIGRVARRDIAAGE 55
>gnl|CDD|225431 COG2876, AroA, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP)
synthase [Amino acid transport and metabolism].
Length = 286
Score = 37.7 bits (88), Expect = 0.005
Identities = 46/211 (21%), Positives = 87/211 (41%), Gaps = 36/211 (17%)
Query: 54 LQQCADQVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLIIST 113
L++ AD+ + MD + +++G+ + N L+K + KP+++
Sbjct: 101 LKRAADETGLPVVTEVMDVRDVEAAAEY-ADILQVGARNMQNFALLKEVGRQNKPVLLKR 159
Query: 114 GMLPSIEHVDNIYTTVKQY---HSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSAYPT 170
G+ +IE + +Y H N +++ C T ++ N
Sbjct: 160 GLSATIEE----WLNAAEYILSHGNGNVILCERGIRT----FEKATRNT----------- 200
Query: 171 PYHDINLNVIHTLR--SRYPDI--PIGYSGHENGVHVCY-AAVAMGAQ--IIEKHFTLDK 223
++++ + L+ + P I P +G + V AA+A GA +IE H +K
Sbjct: 201 ----LDISAVPILKQETHLPVIVDPSHATGRRDLVEPLAKAAIAAGADGLMIEVHPDPEK 256
Query: 224 SWKGSDHASSLTPPELKALVTGIRDIEQSLG 254
+ SD LTP E + LV +R + +LG
Sbjct: 257 AL--SDAKQQLTPEEFEELVKELRALADALG 285
>gnl|CDD|184028 PRK13398, PRK13398, 3-deoxy-7-phosphoheptulonate synthase;
Provisional.
Length = 266
Score = 33.5 bits (77), Expect = 0.13
Identities = 47/205 (22%), Positives = 85/205 (41%), Gaps = 32/205 (15%)
Query: 53 MLQQCADQVDIMFTASAMD--QVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASKQKPLI 110
+L++ D+ ++ MD V ++ ++IGS + N L+K +KP++
Sbjct: 82 ILKEVGDKYNLPVVTEVMDTRDVE---EVADYADMLQIGSRNMQNFELLKEVGKTKKPIL 138
Query: 111 ISTGMLPSIEHVDNIYTTVKQY---HSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSA 167
+ GM ++E + +Y +Y N +++ C T + Y N L V+
Sbjct: 139 LKRGMSATLE--EWLYAA--EYIMSEGNENVVLCERG----IRTFETYTRNTLDLAAVAV 190
Query: 168 YPTPYH-DINLNVIHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQ--IIEKHFTLDKS 224
H I ++ H R IP+ AA+A GA +IE H +K+
Sbjct: 191 IKELSHLPIIVDPSHATGRRELVIPMA-----------KAAIAAGADGLMIEVHPEPEKA 239
Query: 225 WKGSDHASSLTPPELKALVTGIRDI 249
SD +L E+K LV ++ +
Sbjct: 240 L--SDARQTLNFEEMKELVDELKPM 262
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 32.4 bits (75), Expect = 0.27
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 180 IHTLRSRYPDIPIGYSGHEN---GVHVCYAAVAMGAQIIE 216
+ LR PD+P+G H V AA+ GA ++
Sbjct: 181 VKALREALPDVPLGLHTHNTLGLAVANSLAALEAGADRVD 220
>gnl|CDD|233375 TIGR01361, DAHP_synth_Bsub, phospho-2-dehydro-3-deoxyheptonate
aldolase. This model describes one of at least three
types of phospho-2-dehydro-3-deoxyheptonate aldolase
(DAHP synthase). This enzyme catalyzes the first of 7
steps in the biosynthesis of chorismate, that last
common precursor of all three aromatic amino acids and
of PABA, ubiquinone and menaquinone. Some members of
this family, including an experimentally characterized
member from Bacillus subtilis, are bifunctional, with a
chorismate mutase domain N-terminal to this region. The
member of this family from Synechocystis PCC 6803, CcmA,
was shown to be essential for carboxysome formation.
However, no other candidate for this enzyme is present
in that species, chorismate biosynthesis does occur,
other species having this protein lack carboxysomes but
appear to make chorismate, and a requirement of CcmA for
carboxysome formation does not prohibit a role in
chorismate biosynthesis [Amino acid biosynthesis,
Aromatic amino acid family].
Length = 260
Score = 31.9 bits (73), Expect = 0.32
Identities = 21/96 (21%), Positives = 46/96 (47%), Gaps = 11/96 (11%)
Query: 25 RPYLSPHAWANTYGQHKQHLEFSQEEYVMLQQCADQVDIMFTASAMDQVSFDFLLSANVP 84
+P SP+++ G ++ L+ L++ AD+ + MD + +++
Sbjct: 62 KPRTSPYSFQ---GLGEEGLKL-------LRRAADEHGLPVVTEVMDPRDVE-IVAEYAD 110
Query: 85 FIKIGSGDSNNIPLIKYAASKQKPLIISTGMLPSIE 120
++IG+ + N L+K + KP+++ GM +IE
Sbjct: 111 ILQIGARNMQNFELLKEVGKQGKPVLLKRGMGNTIE 146
Score = 31.2 bits (71), Expect = 0.58
Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 206 AAVAMGAQ--IIEKHFTLDKSWKGSDHASSLTPPELKALVTGIRDI 249
AA+A GA +IE H +K+ SD LTP E K LV +R +
Sbjct: 217 AAIAAGADGLMIEVHPDPEKAL--SDSKQQLTPEEFKRLVKELRAL 260
>gnl|CDD|149458 pfam08404, Baculo_p74_N, Baculoviridae P74 N-terminal. This domain
is found at the N-terminus of P74 occlusion-derived
virus (ODV) envelope proteins which are required for
oral infectivity. The envelope proteins are found in
baculoviruses which are insect pathogens. The C-terminus
of P74 is anchored to the membrane whereas the
N-terminus is exposed to the virion surface. Furthermore
P74 is unusual for a virus envelope protein as it lacks
an N-terminal localisation signal sequence. Also see
pfam04583.
Length = 301
Score = 31.1 bits (71), Expect = 0.73
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 172 YHDINLNVIHTLRSRYPDIPIGYS 195
H L I R+++P I I YS
Sbjct: 13 SHRHRLRYIPKWRTKFPHILIDYS 36
>gnl|CDD|224349 COG1432, COG1432, Uncharacterized conserved protein [Function
unknown].
Length = 181
Score = 30.5 bits (69), Expect = 0.79
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 48 QEEYVMLQQCADQVDIMFTASAMDQVSFDFLLSANVPFIKIGSGDSNNIPLIKYAASK-Q 106
+ + L+ VD+ AM+ NV I + SGD + IPL++ A K +
Sbjct: 81 LDGFTDLRITKGDVDVELAVDAMELADKK-----NVDTIVLFSGDGDFIPLVEAARDKGK 135
Query: 107 KPLIISTGMLPSIEHVDNIYTTVK 130
+ + + S + + +
Sbjct: 136 RVEVAGIEPMTSSDLRNAADYYID 159
>gnl|CDD|218407 pfam05061, Pox_A11, Poxvirus A11 Protein. Family of conserved
Chordopoxvirinae A11 family proteins. Conserved region
spans entire protein in the majority of family members.
Length = 309
Score = 30.9 bits (70), Expect = 0.91
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 96 IPLIKYAASKQKPLIISTGMLPSIEHVDNIYTTVKQYH 133
I ++ YA+ PL + + S E +D +Y +KQY+
Sbjct: 188 IAIVNYASLNNSPLTMEDLEVCSDEEIDKMYKVIKQYN 225
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 29.8 bits (68), Expect = 1.7
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 188 PDIPIGYSGHEN---GVHVCYAAVAMGAQII 215
PD +G+ GH N GV AAV GA I
Sbjct: 188 PDTQVGFHGHNNLGLGVANSLAAVEAGATRI 218
>gnl|CDD|176521 cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial glycerophosphodiester
phosphodiesterases. In addition to a C-terminal GDPD
domain, most members in this family have an N-terminus
that functions as a membrane anchor.
Length = 220
Score = 28.7 bits (65), Expect = 3.4
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 6/43 (13%)
Query: 152 VKQYHSNLSILHCVSAYPTPYHDINLNVIHTLRSRYPDIPIGY 194
VK Y NL H ++ VI ++ P I GY
Sbjct: 118 VKLYKQNLIENQHQ------VHSLDYRVIEKVKKLDPKIKTGY 154
>gnl|CDD|218674 pfam05644, Miff, Mitochondrial and peroxisomal fission factor Mff.
This protein has a role in mitochondrial and peroxisomal
fission.
Length = 243
Score = 28.7 bits (64), Expect = 3.6
Identities = 10/43 (23%), Positives = 14/43 (32%)
Query: 132 YHSNLSILHCVSAYPTPYPTVKQYHSNLSILHCVSAYPTPYHD 174
+N + SA T + H+N L TP D
Sbjct: 137 VRNNGQLSRGDSASTTGSAPKRSKHNNELNLTRSLREGTPTLD 179
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 28.6 bits (65), Expect = 3.8
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 180 IHTLRSRYPDIPIGYSGHEN---GVHVCYAAVAMGAQII 215
+ LR P+G+ GH N V AAV GA I
Sbjct: 176 VRALREALDPTPVGFHGHNNLGLAVANSLAAVEAGATRI 214
>gnl|CDD|237376 PRK13396, PRK13396, 3-deoxy-7-phosphoheptulonate synthase;
Provisional.
Length = 352
Score = 28.2 bits (63), Expect = 5.8
Identities = 44/180 (24%), Positives = 75/180 (41%), Gaps = 36/180 (20%)
Query: 86 IKIGSGDSNNIPLIKYAASKQKPLIISTGMLPSIEHVDNIYTTVKQY---HSNLSILHCV 142
I++G+ + N L+K ++ KP+++ GM +I+ + +Y N +++ C
Sbjct: 188 IQVGARNMQNFSLLKKVGAQDKPVLLKRGMAATIDE----WLMAAEYILAAGNPNVILCE 243
Query: 143 SAYPTPYPTVKQYHSNLSILHCVSAYPTPYHDINLNVIHTLRSRYPDIPI------GYSG 196
T +QY N ++L+VI LRS +PI G
Sbjct: 244 RGIRT---FDRQYTRNT---------------LDLSVIPVLRS-LTHLPIMIDPSHGTGK 284
Query: 197 HENGVHVCYAAVAMGAQ--IIEKHFTLDKSWKGSDHASSLTPPELKALVTGIRDIEQSLG 254
E + AA+A G +IE H K+ SD SLTP L+ + I +++G
Sbjct: 285 SEYVPSMAMAAIAAGTDSLMIEVHPNPAKAL--SDGPQSLTPDRFDRLMQELAVIGKTVG 342
>gnl|CDD|225253 COG2378, COG2378, Predicted transcriptional regulator
[Transcription].
Length = 311
Score = 28.1 bits (63), Expect = 5.9
Identities = 21/88 (23%), Positives = 28/88 (31%), Gaps = 27/88 (30%)
Query: 170 TPYHDINLNVIHTLRSRYPDIPIGYSGHENGVHVCYAAVAMGAQIIEKHFTLDKSWKGSD 229
T Y DI TLR+ +PI E G Y + F L
Sbjct: 38 TIYRDIA-----TLRAAG--VPIEG---ERGKGGGY--------RLRPGFKLPPLM---- 75
Query: 230 HASSLTPPELKALVTGIRDIEQSLGSPT 257
T E +AL+ +R + S G
Sbjct: 76 ----FTEEEAEALLLALRALA-SRGGAE 98
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 28.4 bits (64), Expect = 6.8
Identities = 7/35 (20%), Positives = 18/35 (51%)
Query: 39 QHKQHLEFSQEEYVMLQQCADQVDIMFTASAMDQV 73
Q + LE ++E L + +++++ + D+V
Sbjct: 862 QQRSQLEQAKEGLSALNRLLPRLNLLADETLADRV 896
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 27.7 bits (62), Expect = 7.3
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 169 PTPYHDINLNVIHTLRSRYPDIPIGYSGHEN---GVHVCYAAVAMGAQIIE 216
P D+ I L+ R P + I H + V AAV GA ++
Sbjct: 164 PNEAADL----ISALKDRVPPVIIEVHCHNDLGMAVANSLAAVEAGADRVD 210
>gnl|CDD|236661 PRK10177, PRK10177, putative invasin; Provisional.
Length = 465
Score = 28.2 bits (63), Expect = 7.5
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 208 VAMGAQIIEKHFTLDKSWKGSDHASSLTPP 237
V + QI +H SW+G A SLTP
Sbjct: 371 VPLKLQIRSRHGIRQLSWQGDTQALSLTPG 400
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 0.133 0.405
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,381,607
Number of extensions: 1503863
Number of successful extensions: 1195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1173
Number of HSP's successfully gapped: 35
Length of query: 335
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 238
Effective length of database: 6,635,264
Effective search space: 1579192832
Effective search space used: 1579192832
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: 59 (26.4 bits)