RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18055
(95 letters)
>gnl|CDD|215548 PLN03042, PLN03042, Lactoylglutathione lyase; Provisional.
Length = 185
Score = 169 bits (429), Expect = 2e-55
Identities = 76/125 (60%), Positives = 85/125 (68%), Gaps = 30/125 (24%)
Query: 1 MQQTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMG----------------- 43
MQQTM+RIKDP+ SL FY++VLGMSLLK+LDFP MKFSLYF+G
Sbjct: 28 MQQTMFRIKDPKASLDFYSRVLGMSLLKRLDFPEMKFSLYFLGYEDSETAPTDPPERTVW 87
Query: 44 ------------NWGTEKDEDLT-YHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFV 90
NWGTE D + YHNGNSDPRGFGHIGI V DV KACERFE+LGVEFV
Sbjct: 88 TFGRKATIELTHNWGTESDPEFKGYHNGNSDPRGFGHIGITVDDVYKACERFEKLGVEFV 147
Query: 91 KKPND 95
KKP+D
Sbjct: 148 KKPDD 152
>gnl|CDD|177995 PLN02367, PLN02367, lactoylglutathione lyase.
Length = 233
Score = 163 bits (413), Expect = 2e-52
Identities = 79/125 (63%), Positives = 85/125 (68%), Gaps = 30/125 (24%)
Query: 1 MQQTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMG----------------- 43
MQQTMYRIKDP+ SL FY++VLGMSLLK+LDFP MKFSLYFMG
Sbjct: 76 MQQTMYRIKDPKASLDFYSRVLGMSLLKRLDFPEMKFSLYFMGYEDTASAPTDPTERTVW 135
Query: 44 ------------NWGTEKDEDLT-YHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFV 90
NWGTE D D YHNGNS+PRGFGHIGI V DV KACERFE+LGVEFV
Sbjct: 136 TFGQKATIELTHNWGTESDPDFKGYHNGNSEPRGFGHIGITVDDVYKACERFEELGVEFV 195
Query: 91 KKPND 95
KKPND
Sbjct: 196 KKPND 200
>gnl|CDD|176659 cd07233, Glyoxalase_I, Glyoxalase I catalyzes the isomerization of
the hemithioacetal, formed by a 2-oxoaldehyde and
glutathione, to S-D-lactoylglutathione. Glyoxalase I
(also known as lactoylglutathione lyase; EC 4.4.1.5) is
part of the glyoxalase system, a two-step system for
detoxifying methylglyoxal, a side product of glycolysis.
This system is responsible for the conversion of
reactive, acyclic alpha-oxoaldehydes into the
corresponding alpha-hydroxyacids and involves 2 enzymes,
glyoxalase I and II. Glyoxalase I catalyses an
intramolecular redox reaction of the hemithioacetal
(formed from methylglyoxal and glutathione) to form the
thioester, S-D-lactoylglutathione. This reaction
involves the transfer of two hydrogen atoms from C1 to
C2 of the methylglyoxal, and proceeds via an ene-diol
intermediate. Glyoxalase I has a requirement for bound
metal ions for catalysis. Eukaryotic glyoxalase I
prefers the divalent cation zinc as cofactor, whereas
Escherichia coil and other prokaryotic glyoxalase I uses
nickel. However, eukaryotic Trypanosomatid parasites
also use nickel as a cofactor, which could possibly be
explained by acquiring their GLOI gene by horizontal
gene transfer. Human glyoxalase I is a two-domain enzyme
and it has the structure of a domain-swapped dimer with
two active sites located at the dimer interface. In
yeast, in various plants, insects and Plasmodia,
glyoxalase I is four-domain, possibly the result of a
further gene duplication and an additional gene fusing
event.
Length = 121
Score = 135 bits (342), Expect = 7e-43
Identities = 52/109 (47%), Positives = 61/109 (55%), Gaps = 22/109 (20%)
Query: 1 MQQTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMG--------------NWG 46
TM R+KD KSL FYT VLGM LL++ DFP KF+L F+G NWG
Sbjct: 1 FLHTMLRVKDLEKSLDFYTDVLGMKLLRRKDFPEGKFTLVFLGYPDEDSEGVLELTYNWG 60
Query: 47 TEKDEDLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKPND 95
TE+ Y NGN GFGH+ V DV ACER E++GVE K P D
Sbjct: 61 TEE----PYDNGN----GFGHLAFAVDDVYAACERLEEMGVEVTKPPGD 101
>gnl|CDD|232807 TIGR00068, glyox_I, lactoylglutathione lyase. Lactoylglutathione
lyase is also known as aldoketomutase and glyoxalase I.
Glyoxylase I is a homodimer in many species. In some
eukaryotes, including yeasts and plants, the orthologous
protein carries a tandem duplication, is twice as long,
and hits This model twice [Central intermediary
metabolism, Amino sugars, Energy metabolism, Other].
Length = 150
Score = 132 bits (334), Expect = 2e-41
Identities = 54/107 (50%), Positives = 61/107 (57%), Gaps = 23/107 (21%)
Query: 1 MQQTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMG--------------NWG 46
+ TM R+ D KSL FYT+VLGM LL+K DFP MKFSL F+G NWG
Sbjct: 18 LLHTMLRVGDLDKSLDFYTEVLGMKLLRKRDFPEMKFSLAFLGYGDETSAAVIELTHNWG 77
Query: 47 TEKDEDLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
TEK Y GN GFGHI I V DV KACER LG V++P
Sbjct: 78 TEK-----YDLGN----GFGHIAIGVDDVYKACERVRALGGNVVREP 115
>gnl|CDD|216182 pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance
protein/Dioxygenase superfamily.
Length = 120
Score = 67.8 bits (166), Expect = 3e-16
Identities = 28/98 (28%), Positives = 37/98 (37%), Gaps = 6/98 (6%)
Query: 3 QTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDEDLTYHNGNSDP 62
R+ D KSL FYT VLG L++++D F G E L
Sbjct: 4 HVALRVGDLEKSLDFYTDVLGFKLVEEVDDGEGPLRSAFFTA-GGRVLELLLNETPPPAA 62
Query: 63 -----RGFGHIGIQVPDVTKACERFEQLGVEFVKKPND 95
I V DV A +R + GVE V++P
Sbjct: 63 AGFGGHHIAFIAFSVDDVDAAYDRLKAAGVEIVREPGR 100
Score = 24.3 bits (53), Expect = 9.9
Identities = 7/30 (23%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 64 GFGHIGIQVPDVTKACERFEQ-LGVEFVKK 92
H+ ++V D+ K+ + + LG + V++
Sbjct: 1 RIDHVALRVGDLEKSLDFYTDVLGFKLVEE 30
>gnl|CDD|182358 PRK10291, PRK10291, glyoxalase I; Provisional.
Length = 129
Score = 64.3 bits (156), Expect = 8e-15
Identities = 35/88 (39%), Positives = 52/88 (59%), Gaps = 7/88 (7%)
Query: 5 MYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDE---DLTYHNGNSD 61
M R+ D ++S+ FYT VLGM LL+ + P K+SL F+G +G E +E +LTY+ G
Sbjct: 1 MLRVGDLQRSIDFYTNVLGMKLLRTSENPEYKYSLAFVG-YGPETEEAVIELTYNWGVDK 59
Query: 62 ---PRGFGHIGIQVPDVTKACERFEQLG 86
+GHI + V + +ACE+ Q G
Sbjct: 60 YELGTAYGHIALSVDNAAEACEKIRQNG 87
>gnl|CDD|215169 PLN02300, PLN02300, lactoylglutathione lyase.
Length = 286
Score = 66.0 bits (161), Expect = 2e-14
Identities = 37/99 (37%), Positives = 54/99 (54%), Gaps = 7/99 (7%)
Query: 1 MQQTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDE---DLTYHN 57
M +YR+ D +++ FYT+ LGM LL+K D P K++ F+G +G E +LTY+
Sbjct: 25 MLHVVYRVGDLDRTIKFYTECLGMKLLRKRDIPEEKYTNAFLG-YGPEDSNFVVELTYNY 83
Query: 58 GNSD---PRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
G GFGH GI V DV K E + G + ++P
Sbjct: 84 GVDKYDIGTGFGHFGIAVEDVAKTVELVKAKGGKVTREP 122
Score = 55.9 bits (135), Expect = 9e-11
Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 7/97 (7%)
Query: 3 QTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDE---DLTYHNGN 59
Q M R+ D +S+ FY K GM LL+K D P K+++ MG +G E +LTY+ G
Sbjct: 157 QVMLRVGDLDRSIKFYEKAFGMKLLRKRDNPEYKYTIAMMG-YGPEDKTTVLELTYNYGV 215
Query: 60 SD---PRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
++ + I I DV K E + +G + ++P
Sbjct: 216 TEYTKGNAYAQIAIGTDDVYKTAEAIKLVGGKITREP 252
>gnl|CDD|211348 cd06587, Glo_EDI_BRP_like, This domain superfamily is found in a
variety of structurally related metalloproteins,
including the type I extradiol dioxygenases, glyoxalase
I and a group of antibiotic resistance proteins. This
domain superfamily is found in a variety of
structurally related metalloproteins, including the
type I extradiol dioxygenases, glyoxalase I and a group
of antibiotic resistance proteins. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I
extradiol dioxygenases catalyze the incorporation of
both atoms of molecular oxygen into aromatic
substrates, which results in the cleavage of aromatic
rings. They are key enzymes in the degradation of
aromatic compounds. Type I extradiol dioxygenases
include class I and class II enzymes. Class I and II
enzymes show sequence similarity; the two-domain class
II enzymes evolved from a class I enzyme through gene
duplication. Glyoxylase I catalyzes the
glutathione-dependent inactivation of toxic
methylglyoxal, requiring zinc or nickel ions for
activity. The antibiotic resistance proteins in this
family use a variety of mechanisms to block the
function of antibiotics. Bleomycin resistance protein
(BLMA) sequesters bleomycin's activity by directly
binding to it. Whereas, three types of fosfomycin
resistance proteins employ different mechanisms to
render fosfomycin inactive by modifying the fosfomycin
molecule. Although the proteins in this superfamily are
functionally distinct, their structures are similar.
The difference among the three dimensional structures
of the three types of proteins in this superfamily is
interesting from an evolutionary perspective. Both
glyoxalase I and BLMA show domain swapping between
subunits. However, there is no domain swapping for type
1 extradiol dioxygenases.
Length = 110
Score = 50.5 bits (121), Expect = 1e-09
Identities = 26/98 (26%), Positives = 38/98 (38%), Gaps = 13/98 (13%)
Query: 3 QTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGT-----EKDEDLTYHN 57
+ D ++ FY VLG +L++ A F+ GT E DE
Sbjct: 1 HVGLTVPDLEAAVAFYEDVLGFEVLERDGGGAE---FAFLRLGGTRLELFEGDEP----- 52
Query: 58 GNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKPND 95
G H+ +V DV A ER + GVE + P +
Sbjct: 53 APPSGGGGVHLAFEVDDVDAAVERLKAAGVEILGGPRE 90
>gnl|CDD|221708 pfam12681, Glyoxalase_2, Glyoxalase-like domain. This domain is
related to the Glyoxalase domain pfam00903.
Length = 109
Score = 49.0 bits (117), Expect = 5e-09
Identities = 15/91 (16%), Positives = 36/91 (39%), Gaps = 6/91 (6%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKD--EDLTYHNGNSDPRG 64
+ D + FY ++LG +++ +++ + +G E + ++ G
Sbjct: 2 PVSDLEAARAFYEELLGF----EVEEEDGEYAEFRLGLVLALGGFIELIGLPEPDAPGGG 57
Query: 65 FGHIGIQVPDVTKACERFEQLGVEFVKKPND 95
H+ +V D+ R + G ++ P D
Sbjct: 58 GVHLYFEVDDLDALVARLKAAGGTILEPPED 88
>gnl|CDD|223423 COG0346, GloA, Lactoylglutathione lyase and related lyases [Amino
acid transport and metabolism].
Length = 138
Score = 40.5 bits (94), Expect = 2e-05
Identities = 23/112 (20%), Positives = 33/112 (29%), Gaps = 21/112 (18%)
Query: 3 QTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPA----MKFSLYFMGNWGTEKDEDLTYHNG 58
+ D S+ FYT VLG+ L+K A L+ G+ G + G
Sbjct: 5 HVTLAVPDLEASIDFYTDVLGLRLVKDTVNEADDGGGYHLLFLDGDGGPGELLAFFGFEG 64
Query: 59 N--------------SDPRGFGHIGIQVPDVT---KACERFEQLGVEFVKKP 93
G GH+ +V D A + GV
Sbjct: 65 RAGTGFVGDVALGVPGGDLGLGHLAFEVDDEAFGDAALAFLDPDGVRIELGE 116
Score = 26.7 bits (58), Expect = 1.8
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 63 RGFGHIGIQVPDVTKACERFEQ-LGVEFVKK 92
G H+ + VPD+ + + + LG+ VK
Sbjct: 1 MGIHHVTLAVPDLEASIDFYTDVLGLRLVKD 31
>gnl|CDD|176669 cd07245, Glo_EDI_BRP_like_9, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The proteins of this family share three
conserved metal binding amino acids with the type I
extradiol dioxygenases.
Length = 114
Score = 39.1 bits (92), Expect = 3e-05
Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 14/94 (14%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFM--GNW-----GTEKDEDLTYHNGN 59
R+ D S FYT VLG L++ P F ++ G+ E D
Sbjct: 7 RVPDLEASRAFYTDVLG---LEEGPRPPFLFPGAWLYAGDGPQLHLIEEDPPDALPEGPG 63
Query: 60 SDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
D HI +V D+ R + GV + +
Sbjct: 64 RD----DHIAFRVDDLDAFRARLKAAGVPYTESD 93
>gnl|CDD|211356 cd08346, PcpA_N_like, N-terminal domain of Sphingobium
chlorophenolicum 2,6-dichloro-p-hydroquinone
1,2-dioxygenase (PcpA), and similar proteins. The
N-terminal domain of Sphingobium chlorophenolicum
(formerly Sphingomonas chlorophenolica)
2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and
similar proteins. PcpA is a key enzyme in the
pentachlorophenol (PCP) degradation pathway, catalyzing
the conversion of 2,6-dichloro-p-hydroquinone to
2-chloromaleylacetate. This domain belongs to a
conserved domain superfamily that is found in a variety
of structurally related metalloproteins, including the
bleomycin resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases.
Length = 126
Score = 38.4 bits (90), Expect = 8e-05
Identities = 30/100 (30%), Positives = 41/100 (41%), Gaps = 21/100 (21%)
Query: 6 YRIKDPRKSLPFYTKVLGMSLLKK---LDFPAMKFSLYF---MGNWGTEKDEDLTY---- 55
+D ++++ FYT VLG+ L+KK D P L+F +G+ GT LT+
Sbjct: 7 LVTRDAQETVDFYTDVLGLRLVKKTVNQDDPGTYH-LFFGDGLGSPGT----LLTFFEWP 61
Query: 56 HNGNSDPRG---FGHIGIQVPDVTKAC---ERFEQLGVEF 89
G RG HI VP ER GV
Sbjct: 62 DAGPKGRRGPGQIHHIAFSVPSEASLEAWRERLRAAGVPV 101
>gnl|CDD|176661 cd07237, BphC1-RGP6_C_like, C-terminal domain of
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC
1.13.11.39) 1 from Rhodococcus globerulus P6
(BphC1-RGP6) and similar proteins. This subfamily
contains the C-terminal, catalytic, domain of BphC1-RGP6
and similar proteins. BphC catalyzes the extradiol ring
cleavage reaction of 2,3-dihydroxybiphenyl, the third
step in the polychlorinated biphenyls (PCBs) degradation
pathway (bph pathway). This subfamily of BphCs belongs
to the type I extradiol dioxygenase family, which
require a metal in the active site in its catalytic
mechanism. Polychlorinated biphenyl degrading bacteria
demonstrate a multiplicity of BphCs. For example, three
types of BphC enzymes have been found in Rhodococcus
globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes
are type I extradiol dioxygenases. BphC1-RGP6 has an
internal duplication, it is a two-domain dioxygenase
which forms octamers, and has Fe(II) at the catalytic
site. Its C-terminal repeat is represented in this
subfamily. BphC2-RGP6 and BphC3-RGP6 are one-domain
dioxygenases, they belong to a different subfamily of
the ED_TypeI_classII_C (C-terminal domain of type I,
class II extradiol dioxygenases) family.
Length = 154
Score = 35.3 bits (82), Expect = 0.001
Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 15/100 (15%)
Query: 7 RIKDPRKSLPFYTKVLGMSL---LKKLDFPAMKFSLYFMG-NWGTEKDEDLTYHNGNSDP 62
DP ++ FY VLG L + P + F+ N + L G P
Sbjct: 16 ATPDPDEAHAFYRDVLGFRLSDEIDIPLPPGPTARVTFLHCN---GRHHSLALAEGPG-P 71
Query: 63 RGFGHIGIQVP---DVTKACERFEQLGVEFV----KKPND 95
+ H+ ++V DV +A +R G+ + ND
Sbjct: 72 KRIHHLMLEVTSLDDVGRAYDRVRARGIPIAMTLGRHTND 111
>gnl|CDD|211350 cd07249, MMCE, Methylmalonyl-CoA epimerase (MMCE). MMCE, also
called methylmalonyl-CoA racemase (EC 5.1.99.1)
interconverts (2R)-methylmalonyl-CoA and
(2S)-methylmalonyl-CoA. MMCE has been found in bacteria,
archaea, and in animals. In eukaryotes, MMCE is an
essential enzyme in a pathway that converts
propionyl-CoA to succinyl-CoA, and is important in the
breakdown of odd-chain length fatty acids,
branched-chain amino acids, and other metabolites. In
bacteria, MMCE participates in the reverse pathway for
propionate fermentation, glyoxylate regeneration, and
the biosynthesis of polyketide antibiotics. MMCE is
closely related to glyoxalase I and type I extradiol
dioxygenases.
Length = 128
Score = 34.4 bits (80), Expect = 0.002
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 9 KDPRKSLPFYTKVLGMSLLK-KLDFPAMKFSLYFMGNWGTE------KDEDLTYHNGNSD 61
D +L FY VLG+ + + L F+G + D+D
Sbjct: 9 PDLEAALKFYRDVLGVGPWEREEVPSEQGVRLAFLGLGNVQIELIEPLDDDSPIAKFLEK 68
Query: 62 PR-GFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
G HI +V D+ A R + GV +++
Sbjct: 69 RGEGLHHIAFEVDDIDAALARLKAQGVRLLQEG 101
Score = 28.6 bits (65), Expect = 0.25
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 67 HIGIQVPDVTKACERFEQ-LGVEFV 90
HIGI VPD+ A + + LGV
Sbjct: 3 HIGIAVPDLEAALKFYRDVLGVGPW 27
>gnl|CDD|176676 cd07253, Glo_EDI_BRP_like_2, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The proteins of this family share three
conserved metal binding amino acids with the type I
extradiol dioxygenases, which shows no domain swapping.
Length = 125
Score = 33.3 bits (77), Expect = 0.005
Identities = 21/96 (21%), Positives = 34/96 (35%), Gaps = 17/96 (17%)
Query: 7 RIKDPRKSLPFYTKVLGMSL--------LKKLDFPAMKFSLYFMGNWGTEKDEDLTYHNG 58
+ D +L FYT+VLGM + K L F + K +L+ +G
Sbjct: 10 TVADIEATLDFYTRVLGMEVVRFGEEVGRKALRFGSQKINLHPVGGEFEPAAGSPG---- 65
Query: 59 NSDPRGFGHIGIQV-PDVTKACERFEQLGVEFVKKP 93
G + + P + + E GV + P
Sbjct: 66 ----PGSDDLCLITEPPIDELVAHLEAHGVPIEEGP 97
>gnl|CDD|132684 TIGR03645, glyox_marine, lactoylglutathione lyase family protein.
Members of this protein family share homology with
lactoylglutathione lyase (glyoxalase I) and are found
mainly in marine members of the gammaproteobacteria,
including CPS_0532 from Colwellia psychrerythraea 34H.
This family excludes a well-separated, more narrowly
distributed paralogous family, exemplified by CPS_3492
from C. psychrerythraea. The function is of this
protein family is unknown.
Length = 162
Score = 33.6 bits (77), Expect = 0.006
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 62 PRGFGHIGIQVPDVTKACERFEQ-LGVEFVKKPND 95
PR F HIGI VPD+ A + + + LG + P +
Sbjct: 2 PRTFSHIGISVPDLDAAVKFYTEVLGWYLIMPPTE 36
>gnl|CDD|132257 TIGR03213, 23dbph12diox, 2,3-dihydroxybiphenyl 1,2-dioxygenase.
Members of this protein family all have activity as
2,3-dihydroxybiphenyl 1,2-dioxygenase, the third enzyme
of a pathway for biphenyl degradation. Many of the
extradiol ring-cleaving dioxygenases, to which these
proteins belong, act on a range of related substrates.
Note that some members of this family may be found
operons for toluene or naphthalene degradation, where
other activities of the same enzyme may be more
significant; the trusted cutoff for this model is set
relatively high to exclude most such instances [Energy
metabolism, Other].
Length = 286
Score = 33.5 bits (77), Expect = 0.008
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKKLDFPA---MKFSLYFMGNWGTEKDEDLTYHNGNSDPR 63
R+ D +L FYT+VLG L +D PA + YF+ E+ L + G S+ R
Sbjct: 149 RVPDVDAALAFYTEVLGFQLSDVIDLPAGPGVTVRPYFLHC--NERHHSLAFAAGPSEKR 206
Query: 64 GFGHIGIQVP---DVTKACERF 82
H+ ++V DV A +R
Sbjct: 207 -LNHLMLEVDTLDDVGLALDRV 227
>gnl|CDD|211352 cd07255, Glo_EDI_BRP_like_12, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 125
Score = 32.9 bits (76), Expect = 0.008
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKK 29
R+ D +SL FY VLG+ +L++
Sbjct: 9 RVADLERSLAFYQDVLGLEVLER 31
>gnl|CDD|176673 cd07250, HPPD_C_like, C-terminal domain of 4-hydroxyphenylpyruvate
dioxygenase (HppD) and hydroxymandelate Synthase (HmaS).
HppD and HmaS are non-heme iron-dependent dioxygenases,
which modify a common substrate, 4-hydroxyphenylpyruvate
(HPP), but yield different products. HPPD catalyzes the
second reaction in tyrosine catabolism, the conversion
of 4-hydroxyphenylpyruvate to homogentisate
(2,5-dihydroxyphenylacetic acid, HG). HmaS converts HPP
to 4-hydroxymandelate, a committed step in the formation
of hydroxyphenylglycerine, a structural component of
nonproteinogenic macrocyclic peptide antibiotics, such
as vancomycin. If the emphasis is on catalytic
chemistry, HPPD and HmaS are classified as members of a
large family of alpha-keto acid dependent mononuclear
non-heme iron oxygenases most of which require Fe(II),
molecular oxygen, and an alpha-keto acid (typically
alpha-ketoglutarate) to either oxygenate or oxidize a
third substrate. Both enzymes are exceptions in that
they require two, instead of three, substrates, do not
use alpha-ketoglutarate, and incorporate both atoms of
dioxygen into the aromatic product. Both HPPD and HmaS
exhibit duplicate beta barrel topology in their N- and
C-terminal domains which share sequence similarity,
suggestive of a gene duplication. Each protein has only
one catalytic site located in at the C-terminal domain.
This HPPD_C_like domain represents the C-terminal
domain.
Length = 191
Score = 32.1 bits (74), Expect = 0.020
Identities = 23/96 (23%), Positives = 29/96 (30%), Gaps = 24/96 (25%)
Query: 17 FYTKVLGMSLLKKLDFP---------AM-------KFSLYFMGNWGTEK---DEDLTYHN 57
FY KVLG D + + L G K E L Y+
Sbjct: 22 FYRKVLGFHRFWSFDIEDPYSGLRSRVLASPDGKIRIPLN-EPASGKRKSQIQEFLEYYG 80
Query: 58 GNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
G G HI + D+ GVEF+ P
Sbjct: 81 GA----GVQHIALATDDIFATVAALRARGVEFLPIP 112
>gnl|CDD|176696 cd08348, BphC2-C3-RGP6_C_like, The single-domain
2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC
1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6
and BphC3-RGP6, and similar proteins. This subfamily
contains Rhodococcus globerulus P6 BphC2-RGP6 and
BphC3-RGP6, and similar proteins. BphC catalyzes the
extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, yielding
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. This is
the third step in the polychlorinated biphenyls (PCBs)
degradation pathway (bph pathway). This subfamily of
BphCs belongs to the type I extradiol dioxygenase
family, which require a metal in the active site in its
catalytic mechanism. Most type I extradiol dioxygenases
are activated by Fe(II). Polychlorinated biphenyl
degrading bacteria demonstrate a multiplicity of BphCs.
For example, three types of BphC enzymes have been
found in Rhodococcus globerulus (BphC1-RGP6 -
BphC3-RGP6), all three enzymes are type I extradiol
dioxygenases. BphC2-RGP6 and BphC3-RGP6 are one-domain
dioxygenases, which form hexamers. BphC1-RGP6 has an
internal duplication, it is a two-domain dioxygenase
which forms octamers, its two domains do not belong to
this subfamily.
Length = 134
Score = 31.8 bits (73), Expect = 0.021
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 13/94 (13%)
Query: 6 YRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDEDLTYHNGNSDPR-- 63
++D + FY VLG ++ + + F + ++ + G
Sbjct: 7 LYVRDLEAMVRFYRDVLGFTVTDRGPLGGLVFL-----SRDPDEHHQIALITGRPAAPPP 61
Query: 64 ---GFGHIGIQVPDVTKACERFEQL---GVEFVK 91
G HI +V + + +E+L G+ V
Sbjct: 62 GPAGLNHIAFEVDSLDDLRDLYERLRAAGITPVW 95
>gnl|CDD|213772 TIGR03081, metmalonyl_epim, methylmalonyl-CoA epimerase. Members
of this protein family are the enzyme methylmalonyl-CoA
epimerase (EC 5.1.99.1), also called methylmalonyl-CoA
racemase. This enzyme converts (2R)-methylmalonyl-CoA
to (2S)-methylmalonyl-CoA, which is then a substrate
for methylmalonyl-CoA mutase (TIGR00642). It is known
in bacteria, archaea, and as a mitochondrial protein in
animals. It is closely related to lactoylglutathione
lyase (TIGR00068), which is also called glyoxylase I,
and is also a homodimer.
Length = 128
Score = 31.5 bits (72), Expect = 0.023
Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 6 YRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDEDLTYHNGNS----- 60
+ D ++ FY VLG + + + P + F+ G K E L +S
Sbjct: 7 IAVPDLEEAAKFYEDVLGAQVSEIEELPEQGVKVVFI-ALGNTKVELLEPLGEDSPIAKF 65
Query: 61 -DPRGFG--HIGIQVPDVTKACERFEQLGVE 88
+ G G HI I+V D+ A E ++ GV
Sbjct: 66 LEKNGGGIHHIAIEVDDIEAALETLKEKGVR 96
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 32.0 bits (74), Expect = 0.027
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 13/40 (32%)
Query: 64 GFGHIGIQVPDVTKAC-------------ERFEQLGVEFV 90
G G IG +V KA ER QLGVE V
Sbjct: 147 GLGRIGSEVAKRAKAFGMKVIAYDPYISPERAAQLGVELV 186
>gnl|CDD|176677 cd07254, Glo_EDI_BRP_like_20, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and types I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The proteins of this family share three
conserved metal binding amino acids with the type I
extradiol dioxygenases, which shows no domain swapping.
Length = 120
Score = 31.1 bits (71), Expect = 0.029
Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 26/94 (27%)
Query: 13 KSLPFYTKVLGMSLLKK--------LDFPAMKFSLYFMGNWGTEKDEDLTYHNGNSDPRG 64
S+ FY+K+ G+ K L+ P + F L + G
Sbjct: 14 ASIAFYSKLFGVEPTKVRDDYAKFLLEDPRLNFVLNE---------------RPGAPGGG 58
Query: 65 FGHIGIQV---PDVTKACERFEQLGVEFVKKPND 95
H+G+QV +V +A R E G+ K+ +
Sbjct: 59 LNHLGVQVDSAEEVAEAKARAEAAGLPTFKEEDT 92
>gnl|CDD|211353 cd07263, Glo_EDI_BRP_like_16, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 120
Score = 30.6 bits (70), Expect = 0.045
Identities = 20/109 (18%), Positives = 31/109 (28%), Gaps = 26/109 (23%)
Query: 3 QTMYRIKDPRKSLPFYTKVLGMSLLKKLDFPAM----------------KFSLYFMGNWG 46
+ D K+L FYT+ LG + D P L
Sbjct: 1 LVSLYVDDQDKALAFYTEKLG--FEVREDVPMGGGFRWVTVAPPGSPETSLVLA---PPA 55
Query: 47 TEKDEDLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKPND 95
G G + + D+ E + GVEF ++P +
Sbjct: 56 NPAAMASGLQPG-----GTPGLVLVTDDIDATYEELKARGVEFTEEPRE 99
>gnl|CDD|222305 pfam13669, Glyoxalase_4, Glyoxalase/Bleomycin resistance
protein/Dioxygenase superfamily.
Length = 110
Score = 30.3 bits (69), Expect = 0.052
Identities = 19/107 (17%), Positives = 34/107 (31%), Gaps = 24/107 (22%)
Query: 2 QQTMYRIKDPRKSLPFYTKVLGM---------------SLLKKLDFPAMKFSLYFMGNWG 46
+ D + F+ +LG+ + + D PA++ L
Sbjct: 1 HHIGIVVPDLDAAAAFWVDLLGLGPWGDYRDEPQNVDLAFARLGDGPAVEVELI------ 54
Query: 47 TEKDEDLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
+ + ++ + G HI V D+ A R E GV K
Sbjct: 55 -QPLDGESFLDKG--GPGLHHIAYWVDDLDAAVARLEAQGVRVAPKG 98
>gnl|CDD|176671 cd07247, SgaA_N_like, N-terminal domain of Streptomyces griseus
SgaA (suppression of growth disturbance caused by
A-factor at a high concentration under high osmolality
during early growth phase), and similar domains. SgaA
suppresses the growth disturbances caused by high
osmolarity and a high concentration of A-factor, a
microbial hormone, during the early growth phase in
Streptomyces griseus. A-factor
(2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone)
controls morphological differentiation and secondary
metabolism in Streptomyces griseus. It is a chemical
signaling molecule that at a very low concentration
acts as a switch for yellow pigment production, aerial
mycelium formation, streptomycin production, and
streptomycin resistance. The structure and amino acid
sequence of SgaA are closely related to a group of
antibiotics resistance proteins, including bleomycin
resistance protein, mitomycin resistance protein, and
fosfomycin resistance proteins. SgaA might also
function as a streptomycin resistance protein.
Length = 114
Score = 30.2 bits (69), Expect = 0.060
Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 9/90 (10%)
Query: 9 KDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDED---LTYHNGNSDPRGF 65
DP ++ FY V G + + + +++ + T + +
Sbjct: 9 TDPERAKAFYGAVFGWTF-EDMGDGGGDYAV-----FSTGGGAVGGLMKAPEPAAGSPPG 62
Query: 66 GHIGIQVPDVTKACERFEQLGVEFVKKPND 95
+ V DV A R E G + + P D
Sbjct: 63 WLVYFAVDDVDAAAARVEAAGGKVLVPPTD 92
>gnl|CDD|233358 TIGR01327, PGDH, D-3-phosphoglycerate dehydrogenase. This model
represents a long form of D-3-phosphoglycerate
dehydrogenase, the serA gene of one pathway of serine
biosynthesis. Shorter forms, scoring between trusted and
noise cutoff, include SerA from E. coli [Amino acid
biosynthesis, Serine family].
Length = 525
Score = 29.6 bits (67), Expect = 0.19
Identities = 16/45 (35%), Positives = 18/45 (40%), Gaps = 13/45 (28%)
Query: 64 GFGHIGIQVPDVTKAC-------------ERFEQLGVEFVKKPND 95
G G IG V KA ER EQLGVE V ++
Sbjct: 145 GLGRIGSIVAKRAKAFGMKVLAYDPYISPERAEQLGVELVDDLDE 189
>gnl|CDD|173886 cd01951, lectin_L-type, legume lectins. The L-type (legume-type)
lectins are a highly diverse family of carbohydrate
binding proteins that generally display no enzymatic
activity toward the sugars they bind. This family
includes arcelin, concanavalinA, the lectin-like
receptor kinases, the ERGIC-53/VIP36/EMP46 type1
transmembrane proteins, and an alpha-amylase inhibitor.
L-type lectins have a dome-shaped beta-barrel
carbohydrate recognition domain with a curved
seven-stranded beta-sheet referred to as the "front
face" and a flat six-stranded beta-sheet referred to as
the "back face". This domain homodimerizes so that
adjacent back sheets form a contiguous 12-stranded sheet
and homotetramers occur by a back-to-back association of
these homodimers. Though L-type lectins exhibit both
sequence and structural similarity to one another, their
carbohydrate binding specificities differ widely.
Length = 223
Score = 29.3 bits (66), Expect = 0.20
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 54 TYHNGNSDPRGFGHIGIQVP 73
TY N +++ HI I V
Sbjct: 111 TYKNDDNNDPNGNHISIDVN 130
>gnl|CDD|176668 cd07244, FosA, FosA, a Fosfomycin resistance protein, catalyzes
the addition of glutathione to the antibiotic
fosfomycin, making it inactive. This subfamily family
contains FosA, a fosfomycin resistant protein.
Fosfomycin inhibits the enzyme
UDP-N-acetylglucosamine-3-enolpyruvyltransferase
(MurA), which catalyzes the first committed step in
bacterial cell wall biosynthesis. FosA, catalyzes the
addition of glutathione to the antibiotic fosfomycin,
(1R,2S)-epoxypropylphosphonic acid, making it inactive.
FosA is a Mn(II) dependent enzyme. It is evolutionarily
related to glyoxalase I and type I extradiol
dioxygenases.
Length = 121
Score = 28.1 bits (63), Expect = 0.39
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 8 IKDPRKSLPFYTKVLGMSLLKKLD 31
+ D +S+ FY +LG L + D
Sbjct: 9 VSDLERSVAFYVDLLGFKLHVRWD 32
>gnl|CDD|211358 cd08352, Glo_EDI_BRP_like_1, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The proteins of this family share three
conserved metal binding amino acids with the type I
extradiol dioxygenases, which shows no domain swapping.
Length = 125
Score = 27.7 bits (62), Expect = 0.64
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 13/88 (14%)
Query: 10 DPRKSLPFYTKVLGMSLLKKLDFPA---MKFSLYFMGNWGTE------KDEDLTYHNGNS 60
D +S FY +VLG++L+++ P K L G + E +Y
Sbjct: 13 DYARSKEFYVEVLGLTLIRETYRPERKSYKLDLALNGEYQIELFSFPNPPPRPSY----P 68
Query: 61 DPRGFGHIGIQVPDVTKACERFEQLGVE 88
+ G H+ V D+ A + GVE
Sbjct: 69 EACGLRHLAFAVEDIEAAVAELKAHGVE 96
>gnl|CDD|222152 pfam13468, Glyoxalase_3, Glyoxalase-like domain. This domain is
related to the Glyoxalase domain pfam00903.
Length = 174
Score = 27.6 bits (62), Expect = 0.69
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 67 HIGIQVPDVTKACERFEQ-LGVEFV 90
H+ + VPD+ +A RFE LG
Sbjct: 3 HLVVAVPDLDEAVARFEDRLGFTLT 27
Score = 25.7 bits (57), Expect = 4.0
Identities = 5/30 (16%), Positives = 10/30 (33%)
Query: 61 DPRGFGHIGIQVPDVTKACERFEQLGVEFV 90
G ++ D+ R G++F
Sbjct: 74 GGPGLSGWALRTDDIDAVAARLRAAGLDFG 103
>gnl|CDD|218969 pfam06277, EutA, Ethanolamine utilisation protein EutA. This
family consists of several bacterial EutA ethanolamine
utilisation proteins. The EutA protein is thought to
protect the lyase (EutBC) from inhibition by CNB12.
Length = 473
Score = 27.2 bits (61), Expect = 1.4
Identities = 9/36 (25%), Positives = 13/36 (36%)
Query: 52 DLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGV 87
D Y +DP +G IG + + L V
Sbjct: 265 DCIYREEEADPFRYGDIGPLLGKALRRSPDLLSLKV 300
>gnl|CDD|176706 cd08358, Glo_EDI_BRP_like_21, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 127
Score = 26.5 bits (59), Expect = 1.5
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 16/94 (17%)
Query: 6 YRIKDPRKSLPFYTKVLGMSLLKKLDFP---AMKFSLYFMGNW-------GTEKDE---D 52
+++ + K++ FY +VLGM +L+ +F + + G W G E D +
Sbjct: 8 FKVGNRNKTIKFYREVLGMKVLRHEEFEEGCKAACNGPYDGKWSKTMIGYGPEDDHFVVE 67
Query: 53 LTYHNGNSD-PRG--FGHIGIQVPDVTKACERFE 83
LTY+ G D G F I I ++
Sbjct: 68 LTYNYGIGDYELGNDFLGITIHSKQAVSNAKKHN 101
>gnl|CDD|218763 pfam05817, Ribophorin_II, Oligosaccharyltransferase subunit
Ribophorin II. This family contains eukaryotic
Ribophorin II (RPN2) proteins. The mammalian
oligosaccharyltransferase (OST) is a protein complex
that effects the cotranslational N-glycosylation of
newly synthesised polypeptides, and is composed of the
following proteins: ribophorins I and II (RI and RII),
OST48, and Dadl, N33/IAP, OST4, STT3. The family also
includes the SWP1 protein from yeast. In yeast the
oligosaccharyltransferase complex is composed 7 or 8
subunits, SWP1, being one of them.
Length = 636
Score = 26.2 bits (58), Expect = 2.9
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 63 RGFGHIGIQVPDVTKACERFEQL 85
G +GI VPD KAC+ ++
Sbjct: 58 VGLKILGIPVPDEQKACKFVKKN 80
>gnl|CDD|233334 TIGR01263, 4HPPD, 4-hydroxyphenylpyruvate dioxygenase. This
protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and
phenylalanine catabolite, to homogentisate.
Homogentisate can undergo a further non-enzymatic
oxidation and polymerization into brown pigments that
protect some bacterial species from light. A similar
process occurs spontaneously in blood and is hemolytic
(see PMID:8000039). In some bacterial species, this
enzyme has been studied as a hemolysin [Energy
metabolism, Amino acids and amines].
Length = 353
Score = 26.1 bits (58), Expect = 3.2
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 50 DEDLTYHNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKKP 93
+E L ++NG G HI + D+ + GVEF+ P
Sbjct: 228 EEFLEFYNGA----GVQHIALNTDDIVRTVRALRARGVEFLDTP 267
>gnl|CDD|211354 cd07266, HPCD_N_class_II, N-terminal domain of
3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD);
belongs to the type I class II family of extradiol
dioxygenases. This subfamily contains the N-terminal,
non-catalytic, domain of HPCD. HPCD catalyses the
second step in the degradation of
4-hydroxyphenylacetate to succinate and pyruvate. The
aromatic ring of 4-hydroxyphenylacetate is opened by
this dioxygenase to yield the 3,4-diol product,
2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is
a homotetramer and each monomer contains two
structurally homologous barrel-shaped domains at the N-
and C-terminus. The active-site metal is located in the
C-terminal barrel and plays an essential role in the
catalytic mechanism. Most extradiol dioxygenases
contain Fe(II) in their active site, but HPCD can be
activated by either Mn(II) or Fe(II). These enzymes
belong to the type I class II family of extradiol
dioxygenases. The class III 3,4-dihydroxyphenylacetate
2,3-dioxygenases belong to a different superfamily.
Length = 121
Score = 25.7 bits (57), Expect = 3.4
Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 37/104 (35%)
Query: 6 YRIKDPRKSLPFYTKVLGMSLLKKLDFPAMKFSLYFMGNWGTEKDEDLTYHNGNSDPR-- 63
R+ D +S FY +LG+ + TE+D+ Y G +
Sbjct: 10 LRVTDLDRSREFYVDLLGLVV--------------------TEEDDGAIYLRGLEEFIHH 49
Query: 64 ----------GFGHIGIQV---PDVTKACERFEQLG--VEFVKK 92
GH+G +V D+ KA F++LG +V+
Sbjct: 50 SLVLTKAPEPAVGHLGFRVRSEEDLDKAEAFFQELGLPTRWVEA 93
>gnl|CDD|224346 COG1429, CobN, Cobalamin biosynthesis protein CobN and related
Mg-chelatases [Coenzyme metabolism].
Length = 1388
Score = 25.8 bits (57), Expect = 4.5
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 13/39 (33%)
Query: 28 KKLDFPAMKFSLYFMGN--------WGTEKDEDLTYHNG 58
K P ++F GN G DE YH+
Sbjct: 502 KYFVIPGIRF-----GNVFVGPQPPRGWLGDESALYHSP 535
>gnl|CDD|176715 cd09013, BphC-JF8_N_like, N-terminal, non-catalytic, domain of
BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from
Bacillus sp. JF8 and similar proteins.
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes
the extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, a key step in the
polychlorinated biphenyls (PCBs) degradation pathway
(bph pathway). BphC belongs to the type I extradiol
dioxygenase family, which requires a metal ion in the
active site in its catalytic mechanism. Polychlorinated
biphenyl degrading bacteria demonstrate a multiplicity
of BphCs. This subfamily of BphC is represented by the
enzyme purified from the thermophilic biphenyl and
naphthalene degrader, Bacillus sp. JF8. The members in
this family of BphC enzymes may use either Mn(II) or
Fe(II) as cofactors. The enzyme purified from Bacillus
sp. JF8 is Mn(II)-dependent, however, the enzyme from
Rhodococcus jostii RHAI has Fe(II) bound to it.
BphC_JF8 is thermostable and its optimum activity is at
85 degrees C. The enzymes in this family have an
internal duplication. This family represents the
N-terminal repeat.
Length = 121
Score = 25.3 bits (56), Expect = 4.6
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 10 DPRKSLPFYTKVLGMSL 26
P +SL F+T VLG+
Sbjct: 16 KPEESLWFFTDVLGLEE 32
>gnl|CDD|234146 TIGR03211, catechol_2_3, catechol 2,3 dioxygenase. Members of
this family all are enzymes active as catechol 2,3
dioxygenase (1.13.11.2), although some members have
highly significant activity on catechol derivatives
such as 3-methylcatechol, 3-chlorocatechol, and
4-chlorocatechol (see Mars, et al.). This enzyme is
also called metapyrocatechase, as it performs a
meta-cleavage (an extradiol ring cleavage), in contrast
to the ortho-cleavage (intradiol ring
cleavage)performed by catechol 1,2-dioxygenase (EC
1.13.11.1), also called pyrocatechase [Energy
metabolism, Other].
Length = 303
Score = 25.7 bits (57), Expect = 4.8
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 7 RIKDPRKSLPFYTKVLGM 24
R+ D +SL YT VLG+
Sbjct: 11 RVLDLEESLKHYTDVLGL 28
>gnl|CDD|237444 PRK13607, PRK13607, proline dipeptidase; Provisional.
Length = 443
Score = 25.2 bits (56), Expect = 6.1
Identities = 9/15 (60%), Positives = 11/15 (73%), Gaps = 1/15 (6%)
Query: 62 PRGFGH-IGIQVPDV 75
P G GH +G+QV DV
Sbjct: 334 PHGLGHPLGLQVHDV 348
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 24.1 bits (53), Expect = 6.4
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 43 GNWGTEKDEDLTYHNGNSDPRGFGHI 68
N+GT KD DL + PRG+ ++
Sbjct: 20 SNYGTVKDVDLPIDREVNLPRGYAYV 45
>gnl|CDD|211357 cd08349, BLMA_like, Bleomycin binding protein (BLMA) and similar
proteins; BLMA confers bleomycin (Bm) resistance by
directly binding to Bm. BLMA also called Bleomycin
resistance protein, confers Bm resistance by directly
binding to Bm. Bm is a glycopeptide antibiotic produced
naturally by actinomycetes. It is a potent anti-cancer
drug, which acts as a strong DNA-cutting agent, thereby
causing cell death. BLMA is produced by actinomycetes
to protect themselves against their own lethal
compound. BLMA has two identically-folded subdomains,
with the same alpha/beta fold; these two halves have no
sequence similarity. BLMAs are dimers and each dimer
binds to two Bm molecules at the Bm-binding pockets
formed at the dimer interface; two Bm molecules are
bound per dimer. BLMA belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. As for the larger
superfamily, this family contains members with or
without domain swapping.
Length = 112
Score = 24.9 bits (55), Expect = 6.5
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKKLDFP 33
+ D KSL FY VLG + + P
Sbjct: 5 PVSDIEKSLAFYRDVLGFEVDFEHPEP 31
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 2 (Musashi-2) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 79
Score = 24.3 bits (52), Expect = 7.3
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 41 FMGNWGTEKDEDLTYHNGNSDPRGFGHIGIQVPDVT-KACE 80
+ +G +D L + + RGFG + + DV K CE
Sbjct: 23 YFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
>gnl|CDD|182306 PRK10207, PRK10207, dipeptide/tripeptide permease B; Provisional.
Length = 489
Score = 24.8 bits (54), Expect = 8.3
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 8 IKDPRKSLPFYTKVLG 23
I DP ++LP YT V G
Sbjct: 444 ITDPLETLPVYTNVFG 459
>gnl|CDD|238693 cd01399, GlcN6P_deaminase, GlcN6P_deaminase:
Glucosamine-6-phosphate (GlcN6P) deaminase subfamily;
GlcN6P deaminase catalyzes the reversible conversion of
GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium.
The reaction is an aldo-keto isomerization coupled with
an amination or deamination. It is the last step of the
metabolic pathway of N-acetyl-D-glucosamine-6-phosphate
(GlcNAc6P). GlcN6P deaminase is a hexameric enzyme that
is allosterically activated by GlcNAc6P.
Length = 232
Score = 24.8 bits (55), Expect = 8.4
Identities = 9/31 (29%), Positives = 11/31 (35%), Gaps = 10/31 (32%)
Query: 65 FGHIGI----------QVPDVTKACERFEQL 85
F HI I D+ C R+E L
Sbjct: 80 FDHIDIKPENIHIPDGNAADLEAECRRYEAL 110
>gnl|CDD|225312 COG2514, COG2514, Predicted ring-cleavage extradiol dioxygenase
[General function prediction only].
Length = 265
Score = 24.6 bits (54), Expect = 9.5
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 7 RIKDPRKSLPFYTKVLGMSLLKK 29
++D FY ++LG+ +L++
Sbjct: 17 NVRDLDSMTSFYQEILGLQVLEE 39
>gnl|CDD|240368 PTZ00339, PTZ00339, UDP-N-acetylglucosamine pyrophosphorylase;
Provisional.
Length = 482
Score = 24.7 bits (54), Expect = 9.9
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 56 HNGNSDPRGFGHIGIQVPDVTKACERFEQLGVEFVKK 92
HN N +P + I + + K + ++ G+E +KK
Sbjct: 69 HNCNIEPPN-NNTFIDIYEKEKERKELKESGLEIIKK 104
>gnl|CDD|129593 TIGR00502, nagB, glucosamine-6-phosphate isomerase. The set of
proteins recognized by This model includes a closely
related pair from Bacillus subtilis, one of which is
uncharacterized but included as a member of the
orthologous set [Central intermediary metabolism, Amino
sugars].
Length = 259
Score = 24.8 bits (54), Expect = 9.9
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 11/50 (22%)
Query: 46 GTEKDEDLTYHNGNSDPRGFGHIGIQ----------VPDVTKACERFEQL 85
G ++ +YH+ + F HI I+ PD+ C R+E+
Sbjct: 76 GLSEEHPESYHSFMHN-NFFQHIDIKPENINILNGNAPDLEAECRRYEEK 124
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
0.321 0.140 0.432
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,902,914
Number of extensions: 394208
Number of successful extensions: 419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 398
Number of HSP's successfully gapped: 62
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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: 53 (24.2 bits)