RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9876
(193 letters)
>gnl|CDD|238186 cd00305, Cu-Zn_Superoxide_Dismutase, Copper/zinc superoxide
dismutase (SOD). superoxide dismutases catalyse the
conversion of superoxide radicals to molecular oxygen.
Three evolutionarily distinct families of SODs are
known, of which the copper/zinc-binding family is one.
Defects in the human SOD1 gene causes familial
amyotrophic lateral sclerosis (Lou Gehrig's disease).
Cytoplasmic and periplasmic SODs exist as dimers,
whereas chloroplastic and extracellular enzymes exist as
tetramers. Structure supports independent functional
evolution in prokaryotes (P-class) and eukaryotes
(E-class) [PMID:.8176730].
Length = 144
Score = 95.8 bits (239), Expect = 2e-25
Identities = 39/76 (51%), Positives = 52/76 (68%)
Query: 15 PHGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRG 74
HG P D RHAGDLG+I ADK+G ++ + D ++SL G +I+GR +VVH DDLG+G
Sbjct: 68 KHGGPNDEGRHAGDLGNIVADKDGVATVSVLDPLISLKGGNSIIGRSLVVHAGQDDLGKG 127
Query: 75 DNAESVKTGNAGARLA 90
+ S TGNAG R+A
Sbjct: 128 PDELSGGTGNAGVRVA 143
Score = 81.9 bits (203), Expect = 3e-20
Identities = 38/66 (57%), Positives = 44/66 (66%), Gaps = 4/66 (6%)
Query: 122 AVAILNGKD--VKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQGCASMGP 179
AVA+L G D V GTV F Q G V I+G ++GLTPG HGFHIHE GD + GC S G
Sbjct: 3 AVAVLKGPDGKVVGTVTFTQQ--SGGVTITGELSGLTPGLHGFHIHEFGDCTNGCTSAGG 60
Query: 180 HYNPFN 185
H+NPF
Sbjct: 61 HFNPFG 66
>gnl|CDD|215700 pfam00080, Sod_Cu, Copper/zinc superoxide dismutase (SODC).
superoxide dismutases (SODs) catalyze the conversion of
superoxide radicals to hydrogen peroxide and molecular
oxygen. Three evolutionarily distinct families of SODs
are known, of which the copper/zinc-binding family is
one. Defects in the human SOD1 gene cause familial
amyotrophic lateral sclerosis (Lou Gehrig's disease).
Structure is an eight-stranded beta sandwich, similar to
the immunoglobulin fold.
Length = 140
Score = 85.0 bits (211), Expect = 2e-21
Identities = 36/76 (47%), Positives = 47/76 (61%), Gaps = 6/76 (7%)
Query: 15 PHGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRG 74
HG P D RHAGDLG+I D +G ++I D ++L G +I+GR +V+H DDL
Sbjct: 67 KHGGPNDEGRHAGDLGNIVVDADGVAKVEIVDDRVTLSGGDSIIGRSLVIHAGEDDL--- 123
Query: 75 DNAESVKTGNAGARLA 90
+S TGNAGARLA
Sbjct: 124 ---KSQPTGNAGARLA 136
Score = 83.8 bits (208), Expect = 6e-21
Identities = 35/66 (53%), Positives = 42/66 (63%), Gaps = 3/66 (4%)
Query: 122 AVAIL--NGKDVKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQGCASMGP 179
AVA+L G V GTV F Q G VL++ +++GL PG HGFHIHE GD S GC S G
Sbjct: 1 AVAVLKGAGGKVVGTVTFTQ-VGGGGVLVTVDLSGLPPGKHGFHIHEFGDCSPGCTSAGG 59
Query: 180 HYNPFN 185
H+NP
Sbjct: 60 HFNPDG 65
>gnl|CDD|166027 PLN02386, PLN02386, superoxide dismutase [Cu-Zn].
Length = 152
Score = 78.0 bits (192), Expect = 1e-18
Identities = 39/75 (52%), Positives = 50/75 (66%)
Query: 16 HGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRGD 75
HGAP D +RHAGDLG++T +G + I D + L GP +I+GR VVVH DDLG+G
Sbjct: 70 HGAPEDENRHAGDLGNVTVGDDGTATFTIVDKQIPLTGPNSIVGRAVVVHADPDDLGKGG 129
Query: 76 NAESVKTGNAGARLA 90
+ S TGNAG R+A
Sbjct: 130 HELSKSTGNAGGRVA 144
Score = 66.5 bits (162), Expect = 3e-14
Identities = 33/65 (50%), Positives = 46/65 (70%), Gaps = 2/65 (3%)
Query: 120 IMAVAILNGKD-VKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQGCASMG 178
+ AVA+LN + VKGT+ F Q + GP ++G+++GL PG HGFH+H GD + GC S G
Sbjct: 2 VKAVAVLNSSEGVKGTIFFTQ-EGDGPTTVTGSLSGLKPGLHGFHVHALGDTTNGCMSTG 60
Query: 179 PHYNP 183
PH+NP
Sbjct: 61 PHFNP 65
>gnl|CDD|178248 PLN02642, PLN02642, copper, zinc superoxide dismutase.
Length = 164
Score = 71.3 bits (174), Expect = 7e-16
Identities = 37/75 (49%), Positives = 48/75 (64%)
Query: 16 HGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRGD 75
HG P + +RHAGDLG+I A +G + I D + L G +ILGR VVVH DDLG+G
Sbjct: 76 HGPPNEEERHAGDLGNILAGSDGVAEILIKDKHIPLSGQYSILGRAVVVHADPDDLGKGG 135
Query: 76 NAESVKTGNAGARLA 90
+ S TGNAG+R+
Sbjct: 136 HKLSKSTGNAGSRVG 150
Score = 62.0 bits (150), Expect = 2e-12
Identities = 33/69 (47%), Positives = 46/69 (66%), Gaps = 2/69 (2%)
Query: 118 GPIMAVAILNG-KDVKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQGCAS 176
G + AVA++ G +V+G + F+Q G ++G I+GL+PG HGFHIH GD + GC S
Sbjct: 6 GNLRAVALIAGDNNVRGCLQFVQ-DIFGTTHVTGKISGLSPGFHGFHIHSFGDTTNGCIS 64
Query: 177 MGPHYNPFN 185
GPH+NP N
Sbjct: 65 TGPHFNPLN 73
>gnl|CDD|224943 COG2032, SodC, Cu/Zn superoxide dismutase [Inorganic ion transport
and metabolism].
Length = 179
Score = 64.3 bits (157), Expect = 4e-13
Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 15 PHGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRG 74
HG P HAGDL ++ + +G +L + L L G L + GR +V+H DD
Sbjct: 103 KHGGPNADGGHAGDLPNLFVNADGKATLPVLAPRLKLKGLLEVKGRALVIHAGGDDYSTQ 162
Query: 75 DNAESVKTGNAGARLA 90
G AGAR+A
Sbjct: 163 PE----PLGGAGARVA 174
Score = 46.6 bits (111), Expect = 9e-07
Identities = 26/66 (39%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 126 LNGKDVKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQG------CASMGP 179
GKDV GTV + +L + + GL PG+HGFHIHEKG + S G
Sbjct: 38 GTGKDV-GTVTITET--GYGLLFTPALGGLPPGEHGFHIHEKGSCTPKDGKPVDFLSAGG 94
Query: 180 HYNPFN 185
H++P N
Sbjct: 95 HFDPQN 100
>gnl|CDD|215516 PLN02957, PLN02957, copper, zinc superoxide dismutase.
Length = 238
Score = 56.7 bits (137), Expect = 4e-10
Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 122 AVAILNGKDVKGTVLFLQPKPQGPVLISGNITGLTPGDHGFHIHEKGDISQGCASMGPHY 181
AVA G D+ G V F Q + I +GL+PG HG+ I+E GD+++G AS G Y
Sbjct: 83 AVAEFKGPDIFGVVRFAQVSME-LARIEAAFSGLSPGTHGWSINEYGDLTRGAASTGKVY 141
Query: 182 NPFN 185
NP +
Sbjct: 142 NPSD 145
Score = 35.9 bits (83), Expect = 0.006
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 2 DLTGGLNQVYLIY-PHGAPTDPDRHAGDLGSITADKNGFVSLQISDHVLSLDGPLTILGR 60
DLT G +Y P TD + GDLG++ AD+NG + + L + ++GR
Sbjct: 129 DLTRGAASTGKVYNPSDDDTD-EEPLGDLGTLEADENGEATFSGTKEKLKV---WDLIGR 184
Query: 61 GVVVHEKADDLGRG 74
+ V+ AD G G
Sbjct: 185 SLAVYATADKSGPG 198
>gnl|CDD|182357 PRK10290, PRK10290, superoxide dismutase; Provisional.
Length = 173
Score = 32.9 bits (75), Expect = 0.059
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 151 NITGLTPGDHGFHIHEKGD----ISQGCAS----MGPHYNPFN 185
++ L PG+HGFHIH KG G AS G H +P N
Sbjct: 55 DLKALPPGEHGFHIHAKGSCQPATKDGKASAAEAAGGHLDPQN 97
>gnl|CDD|182931 PRK11055, galM, galactose-1-epimerase; Provisional.
Length = 342
Score = 31.4 bits (72), Expect = 0.21
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 119 PIMAVAILNG--KDVKGTVL-FLQPKPQGPVLISGNITGLTPG-DHGFHIHEKGDISQGC 174
P+ I NG K V GT F QPK ++ + G DH F + KGD +
Sbjct: 197 PVDEGGIPNGGLKSVAGTSFDFRQPKTIAQDFLADDDQQKVKGYDHAFLLQAKGDGKKPA 256
Query: 175 AS 176
A
Sbjct: 257 AH 258
>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
protein. Members of this protein family are
uncharacterized and contain two copies of the cyclic
nucleotide-binding domain pfam00027. Members are
restricted to select cyanobacteria but are found
regularly in association with a transport operon that,
in turn, is associated with the production of putative
bacteriocins. The models describing the transport operon
are TIGR03794, TIGR03796, and TIGR03797.
Length = 317
Score = 28.7 bits (64), Expect = 1.9
Identities = 12/54 (22%), Positives = 21/54 (38%)
Query: 92 FIHKNPGLNPALLGLDGNWNLMLTVTGPIMAVAILNGKDVKGTVLFLQPKPQGP 145
IH+ ++ + L G +L ++ GP V ++ G FL G
Sbjct: 172 LIHEGGTVDALYILLYGEASLSISPDGPGREVGSSRRGEILGETPFLNGSLPGT 225
>gnl|CDD|184293 PRK13742, PRK13742, replication protein; Provisional.
Length = 245
Score = 28.4 bits (63), Expect = 2.2
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 6/77 (7%)
Query: 38 GFVSLQISDHVLSLDGPLTILGRGVVVHEKADDLGRGDNAES----VKTGNAGARLAQFI 93
G S + S + G+ VV + +D G ES +K ++ +R +
Sbjct: 72 GLTSAEASKDIRQALKSFA--GKEVVFYRPEEDAGDEKGYESFPWFIKRAHSPSRGLYSV 129
Query: 94 HKNPGLNPALLGLDGNW 110
H NP L P +GL +
Sbjct: 130 HINPYLIPFFIGLQNRF 146
>gnl|CDD|217394 pfam03155, Alg6_Alg8, ALG6, ALG8 glycosyltransferase family.
N-linked (asparagine-linked) glycosylation of proteins
is mediated by a highly conserved pathway in eukaryotes,
in which a lipid (dolichol phosphate)-linked
oligosaccharide is assembled at the endoplasmic
reticulum membrane prior to the transfer of the
oligosaccharide moiety to the target asparagine
residues. This oligosaccharide is composed of
Glc(3)Man(9)GlcNAc(2). The addition of the three glucose
residues is the final series of steps in the synthesis
of the oligosaccharide precursor. Alg6 transfers the
first glucose residue, and Alg8 transfers the second
one. In the human alg6 gene, a C->T transition, which
causes Ala333 to be replaced with Val, has been
identified as the cause of a congenital disorder of
glycosylation, designated as type Ic OMIM:603147.
Length = 463
Score = 28.1 bits (63), Expect = 3.3
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 135 VLFLQPKPQGPVLISGNITGLTPGDHGFHIHEK 167
LFL+P +G L++ + GL+ FH+HEK
Sbjct: 301 KLFLRPTKKG-FLLALTLCGLSFFLFSFHVHEK 332
>gnl|CDD|185286 PRK15388, PRK15388, Cu/Zn superoxide dismutase; Provisional.
Length = 177
Score = 27.0 bits (59), Expect = 5.6
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 146 VLISGNITGLTPGDHGFHIH 165
+L + ++ GLTPG HGFH+H
Sbjct: 52 LLFTPHLNGLTPGIHGFHVH 71
>gnl|CDD|218814 pfam05932, CesT, Tir chaperone protein (CesT) family. This
family consists of a number of bacterial sequences
which are highly similar to the Tir chaperone protein
in E. Coli. In many Gram-negative bacteria, a key
indicator of pathogenic potential is the possession of
a specialised type III secretion system, which is
utilised to deliver virulence effector proteins
directly into the host cell cytosol. Many of the
proteins secreted from such systems require small
cytosolic chaperones to maintain the secreted
substrates in a secretion-competent state. CesT serves
a chaperone function for the enteropathogenic
Escherichia coli (EPEC) translocated intimin receptor
(Tir) protein, which confers upon EPEC the ability to
alter host cell morphology following intimate bacterial
attachment. This family also contains several DspF and
related sequences from several plant pathogenic
bacteria. The "disease-specific" (dsp) region next to
the hrp gene cluster of Erwinia amylovora is required
for pathogenicity but not for elicitation of the
hypersensitive reaction. DspF and AvrF are small (16
kDa and 14 kDa) and acidic with predicted amphipathic
alpha helices in their C termini; they resemble
chaperones for virulence factors secreted by type III
secretion systems of animal pathogens.
Length = 119
Score = 26.5 bits (59), Expect = 5.6
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 29 LGSITADKNGFVSLQISDHVLSLDGP 54
LG + D+NG +L+I + L+ P
Sbjct: 12 LGPLALDENGVCALRIDGEAVVLELP 37
>gnl|CDD|200468 cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family
found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. The
catalytic triad (DED) which is highly conserved in the
other maltase group is not present in this subfamily.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 477
Score = 27.0 bits (60), Expect = 7.4
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 148 ISGNITGLTPGDHGFHIHEK 167
IS N G+TP D+GF+ H K
Sbjct: 249 ISSNTKGVTPNDYGFYTHIK 268
>gnl|CDD|118950 pfam10429, Mtr2, Nuclear pore RNA shuttling protein Mtr2. Mtr2 is
a monomeric, dual-action, RNA-shuttle protein found in
yeasts. Transport across the nuclear-cytoplasmic
membrane is via the macro-molecular membrane-spanning
nuclear pore complex, NPC. The pore is lined by a subset
of NPC members called nucleoporins that present FG
(Phe-Gly) receptors, characteristically GLFG and FXFG
motifs, for shuttling RNAs and proteins. RNA cargo is
bound to soluble transport proteins (nuclear export
factors) such as Mex67 in yeasts, and TAP in metazoa,
which pass along the pore by binding to successive FG
receptors. Mtr2 when bound to Mex67 maximises this
FG-binding. Mtr2 also acts independently of Mex67 in
transporting the large ribosomal RNA subunit through the
pore.
Length = 166
Score = 26.3 bits (58), Expect = 7.7
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 125 ILNGKDVKGTVLFLQPKPQGPVLISGNITG----LTPGDHGFHIH 165
I+NG+ + FLQ Q PVL +T + PG +
Sbjct: 41 IVNGQPFAPPLAFLQKWLQQPVLTQHQLTSFDYHVIPGTGTLICN 85
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
0.317 0.140 0.424
Gapped
Lambda K H
0.267 0.0642 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,958,406
Number of extensions: 934617
Number of successful extensions: 712
Number of sequences better than 10.0: 1
Number of HSP's gapped: 708
Number of HSP's successfully gapped: 29
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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 (21.6 bits)
S2: 56 (25.5 bits)