RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1687
(107 letters)
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 167 bits (426), Expect = 6e-54
Identities = 57/91 (62%), Positives = 70/91 (76%)
Query: 9 QVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSL 68
+VI+RF + +KT FVVEHD IM YL+DR+IVFEG PS++ +AN PQ+L +GMN+FL
Sbjct: 156 KVIRRFAENNEKTAFVVEHDIIMIDYLADRLIVFEGEPSVNGVANPPQSLRSGMNRFLKN 215
Query: 69 LGITFRRDPNNFRPRINKNNSVKDCEQKRAG 99
L ITFRRDP RPRINK SVKD EQK +G
Sbjct: 216 LDITFRRDPETGRPRINKLGSVKDREQKESG 246
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 155 bits (395), Expect = 2e-46
Identities = 49/95 (51%), Positives = 64/95 (67%)
Query: 10 VIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSLL 69
VI+RFI + +KT VV+HD M Y+SDR+IVFEG P A+ P ++ GMN+FL L
Sbjct: 497 VIRRFIENNEKTALVVDHDIYMIDYVSDRLIVFEGEPGKHGHASPPMSMREGMNRFLKNL 556
Query: 70 GITFRRDPNNFRPRINKNNSVKDCEQKRAGQYFFY 104
G+TFRRDP RPR+NK S D EQK G+Y++
Sbjct: 557 GVTFRRDPETGRPRVNKPGSQLDREQKERGEYYYA 591
Score = 40.0 bits (94), Expect = 7e-05
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 13 RFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSLLG-- 70
R + K VVEHD + YLSD V + G P + + + P+++ G+N++L G
Sbjct: 257 RELAEDGKYVIVVEHDLAVLDYLSDFVHILYGEPGVYGVVSKPKSVRVGINEYLK--GYL 314
Query: 71 ----ITFRRDPNNFR 81
+ FR + F
Sbjct: 315 PEENVRFRPEEIEFE 329
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 138 bits (350), Expect = 8e-40
Identities = 44/96 (45%), Positives = 59/96 (61%)
Query: 10 VIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSLL 69
I+R + T VV+HD M Y+SDR++VFEG P A+ P ++ GMN+FL L
Sbjct: 495 AIRRIAEEREATALVVDHDIYMIDYISDRLMVFEGEPGKHGHASGPMDMREGMNRFLKEL 554
Query: 70 GITFRRDPNNFRPRINKNNSVKDCEQKRAGQYFFYE 105
GITFRRD RPR+NK S D EQK G+Y++ +
Sbjct: 555 GITFRRDEETGRPRVNKPGSYLDREQKERGEYYYAD 590
Score = 34.4 bits (80), Expect = 0.005
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 9 QVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLS 67
++I+ L K VVEHD + YL+D V + G P + + P+ + G+N++L
Sbjct: 253 RLIRE--LAEGKYVLVVEHDLAVLDYLADNVHIAYGEPGAYGVVSKPKGVRVGINEYLK 309
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of RNase
L inhibitor. The ABC ATPase RNase L inhibitor (RLI) is
a key enzyme in ribosomal biogenesis, formation of
translation preinitiation complexes, and assembly of HIV
capsids. RLI's are not transport proteins, and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains, which
are arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity more than 48%. The high degree of evolutionary
conservation suggests that RLI performs a central role
in archaeal and eukaryotic physiology.
Length = 177
Score = 101 bits (254), Expect = 8e-29
Identities = 30/66 (45%), Positives = 40/66 (60%)
Query: 9 QVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSL 68
+ I+R KKT VVEHD + YLSDR+ VFEG P + +A+ P+ G+N+FL
Sbjct: 112 RAIRRLSEEGKKTALVVEHDLAVLDYLSDRIHVFEGEPGVYGIASQPKGTREGINRFLRG 171
Query: 69 LGITFR 74
ITFR
Sbjct: 172 YLITFR 177
>gnl|CDD|213203 cd03236, ABC_RNaseL_inhibitor_domain1, The ATP-binding cassette
domain 1 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI s are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLIs have an N-terminal Fe-S domain and
two nucleotide binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 255
Score = 40.0 bits (94), Expect = 5e-05
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 9 QVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLSL 68
++I+ VVEHD + YLSD + G P + P+++ G+N+FL
Sbjct: 180 RLIRELAEDDNYV-LVVEHDLAVLDYLSDYIHCLYGEPGAYGVVTLPKSVREGINEFLD- 237
Query: 69 LGITFRRDPN-NFRP 82
+ N FR
Sbjct: 238 ---GYLPTENMRFRE 249
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 220
Score = 32.1 bits (74), Expect = 0.033
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 17 HAKKTGFVVEHDFIMATYLSDRVIVFEGSP 46
KT +V HD A +L+DRV+V P
Sbjct: 180 ETGKTVLLVTHDIDEAVFLADRVVVLSARP 209
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 30.6 bits (70), Expect = 0.096
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 19 KKTGFVVEHDFIMATYLSDRVIVFEGSPSI 48
+KT +V HD A YL+DRV+V P
Sbjct: 181 RKTVLLVTHDVDEAVYLADRVVVLSNRPGR 210
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 29.7 bits (68), Expect = 0.18
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 8 LQVIKRFILHAK-KTGFVVEHDFIMATYLSDRVIVFE 43
L+++K+ L A+ KT +V HD + L+DRVIV E
Sbjct: 174 LELLKK--LKAEGKTIIIVTHDLDLLLELADRVIVLE 208
>gnl|CDD|129611 TIGR00520, asnASE_II, L-asparaginase, type II. Two related
families of asparaginase (L-asparagine amidohydrolase,
EC 3.5.1.1) are designated type I and type II according
to the terminology in E. coli, which has both:
L-asparaginase I is a low-affinity enzyme found in the
cytoplasm, while L-asparaginase II is a high-affinity
periplasmic enzyme synthesized with a cleavable signal
sequence. This model describes L-asparaginases related
to type II of E. coli. Both the cytoplasmic and the cell
wall asparaginases of Saccharomyces cerevisiae belong to
this set. Members of this set from Acinetobacter
glutaminasificans and Pseudomonas fluorescens are
described as having both glutaminase and asparaginase
activitities. All members are homotetrameric [Energy
metabolism, Amino acids and amines].
Length = 349
Score = 29.7 bits (67), Expect = 0.23
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 22 GFVVEHD---------FIMATYLSDRVIVFEGS--PSISTLANAPQNLLN 60
G V+ H F+ T SD+ +V G+ PS S A+ P NL N
Sbjct: 108 GIVITHGTDTLEETAYFLDLTVKSDKPVVIVGAMRPSTSVSADGPMNLYN 157
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 28.8 bits (65), Expect = 0.39
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 8 LQVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFE 43
L+++K+ KT +V HD + +DRV+V +
Sbjct: 178 LELLKKLKEEGGKTIIIVTHDLELVLEYADRVVVLD 213
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 28.8 bits (65), Expect = 0.44
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 24 VVEHDFIMATYLSDRVIVFE 43
+ HD + ++ DR+ V +
Sbjct: 197 FISHDLALVEHMCDRIAVMD 216
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 28.4 bits (64), Expect = 0.50
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 8 LQVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFE 43
L++++ +T +V HD +A +DRVIV +
Sbjct: 120 LELLRELAEE-GRTVIIVTHDPELAELAADRVIVLK 154
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 27.5 bits (62), Expect = 1.2
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 8 LQVIKRFILHAKKTG---FVVEHDFIMATYLSDRVIV 41
L ++K ++ G + HD + L+DRV+V
Sbjct: 194 LDLLKDLQ---RELGMAVLFITHDLGVVAELADRVVV 227
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent) systems
that are largely represented in archaea and eubacteria
and are primarily involved in scavenging solutes from
the environment. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 178
Score = 27.2 bits (61), Expect = 1.5
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 19 KKTGFVVEHDFIMATYLSDRVIVFE 43
T +V HD A L+DRV+V
Sbjct: 151 GITVVLVTHDLDEAARLADRVVVLR 175
>gnl|CDD|149172 pfam07948, Nairovirus_M, Nairovirus M polyprotein-like. The
sequences in this family are similar to the Dugbe virus
M polyprotein precursor, which includes glycoproteins G1
and G2. Both are thought to be inserted in the membrane
of the Golgi complex of the infected host cell, and G1
is known to have a role in infection of vertebrate
hosts.
Length = 645
Score = 27.5 bits (61), Expect = 1.5
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 47 SISTLANAPQNLLNGMNKFLSLLGITFRRDPN---NFRPRINKNNSVKDCEQKRAGQYF 102
+ + PQ L +K L LLG+T D + RI + ++R ++F
Sbjct: 10 EVRIILTLPQGLKKYYSKILKLLGLTLEEDSEGLLEWCTRILGQVCDDNYFKERIAEFF 68
>gnl|CDD|223330 COG0252, AnsB, L-asparaginase/archaeal Glu-tRNAGln amidotransferase
subunit D [Amino acid transport and metabolism /
Translation, ribosomal structure and biogenesis].
Length = 351
Score = 26.5 bits (59), Expect = 2.8
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 17/53 (32%)
Query: 22 GFVVEH------------DFIMATYLSDRVIVFEGS--PSISTLANAPQNLLN 60
G V+ H T + + +V G+ P+ + ++ P NL N
Sbjct: 103 GVVITHGTDTMEETAFFLSL---TLNTPKPVVLTGAMRPADAPSSDGPANLRN 152
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette transport
system involved in resistant to organic solvents. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 235
Score = 26.3 bits (59), Expect = 2.9
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 10 VIKRFILHAKK----TGFVVEHDFIMATYLSDRV-------IVFEGSP 46
VI I KK T +V HD A ++DR+ IV EG+P
Sbjct: 174 VIDDLIRSLKKELGLTSIMVTHDLDTAFAIADRIAVLYDGKIVAEGTP 221
>gnl|CDD|236519 PRK09442, panF, sodium/panthothenate symporter; Provisional.
Length = 483
Score = 26.0 bits (58), Expect = 3.9
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 6 LTLQVI-KRFILHAKKTGFVVEHDFIMATYLSDRVIVF 42
L+L ++ K+F + A+K V +D + A Y S ++
Sbjct: 89 LSLGILGKKFAILARKYNAVTLNDMLRARYQSRLLVWL 126
>gnl|CDD|212037 cd10327, SLC5sbd_PanF, Na(+)/pantothenate cotransporters: PanF of
Escherichia coli and related proteins; solute binding
domain. PanF catalyzes the Na+-coupled uptake of
extracellular pantothenate for coenzyme A biosynthesis
in cells. This subfamily belongs to the solute carrier 5
(SLC5) transporter family.
Length = 472
Score = 26.0 bits (58), Expect = 4.3
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 6 LTLQVI-KRFILHAKKTGFVVEHDFIMATYLSDRVIVF 42
LTL V+ K+F + A+K V D++ A Y S ++V
Sbjct: 87 LTLGVLGKKFAIIARKINAVTIIDYLRARYNSKALVVL 124
>gnl|CDD|211384 cd11298, O-FucT-2, GDP-fucose protein O-fucosyltransferase 2.
O-FucT-2 adds O-fucose to thrombospondin type 1 repeats
(TSRs), and appears conserved in bilateria. The
O-fucosylation of TSRs appears to play a role in
regulating secretion of metalloproteases of the ADAMTS
superfamily. O-fucosyltransferase-like proteins are
GDP-fucose dependent enzymes with similarities to the
family 1 glycosyltransferases (GT1). They are soluble ER
proteins that may be proteolytically cleaved from a
membrane-associated preprotein, and are involved in the
O-fucosylation of protein substrates, the core
fucosylation of growth factor receptors, and other
processes.
Length = 374
Score = 25.7 bits (57), Expect = 4.9
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 80 FRPRINKNNSVKDCEQKRAGQYFFYEE 106
R I + KDC+ K G ++ Y E
Sbjct: 117 ERSCIIEPVYSKDCDGKYRGWFWGYCE 143
>gnl|CDD|176874 cd08865, SRPBCC_10, Ligand-binding SRPBCC domain of an
uncharacterized subfamily of proteins. Uncharacterized
group of the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
SRPBCC domains include the steroidogenic acute
regulatory protein (StAR)-related lipid transfer
(START) domains of mammalian STARD1-STARD15, the
C-terminal catalytic domains of the alpha oxygenase
subunit of Rieske-type non-heme iron aromatic
ring-hydroxylating oxygenases (RHOs_alpha_C), Class I
and II phosphatidylinositol transfer proteins (PITPs),
Bet v 1 (the major pollen allergen of white birch,
Betula verrucosa), CoxG, CalC, and related proteins.
Other members of the superfamily include PYR/PYL/RCAR
plant proteins, the aromatase/cyclase (ARO/CYC) domains
of proteins such as Streptomyces glaucescens
tetracenomycin, and the SRPBCC domains of Streptococcus
mutans Smu.440 and related proteins.
Length = 140
Score = 25.3 bits (56), Expect = 5.4
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 13 RFILHAKKTGFVVEHDFIMATYLSDRVIVFEGS 45
R+ K G +E + + Y R +VF GS
Sbjct: 47 RYHQVRKFLGRRIELTYEITEYEPGRRVVFRGS 79
>gnl|CDD|114751 pfam06047, SynMuv_product, Ras-induced vulval development
antagonist. This family is from synthetic multi-vulval
genes which encode chromatin-associated proteins
involved in transcriptional repression. This protein has
a role in antagonising Ras-induced vulval development.
Length = 105
Score = 25.1 bits (55), Expect = 5.8
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 83 RINKNNSVKDCEQKRAGQYFFYEE 106
RI K N V E+KRA F YEE
Sbjct: 63 RIRKENQVYSAEEKRALAMFNYEE 86
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 25.6 bits (57), Expect = 5.9
Identities = 8/34 (23%), Positives = 17/34 (50%)
Query: 8 LQVIKRFILHAKKTGFVVEHDFIMATYLSDRVIV 41
L++++ T +V HD +A +D +I+
Sbjct: 178 LELLRDLNREKGLTVVMVLHDLNLAARYADHLIL 211
>gnl|CDD|212087 cd11518, SLC6sbd_SIT1, Na(+)- and Cl(-)-dependent imino acid
transporter SIT1; solute-binding domain. SIT1 (also
called XTRP3, XT3, IMINO) transports imino acids, such
as proline, pipecolate, MeAIB, and sarcosine. It has
weak affinity for neutral amino acids such as
phenylalanine. Human SIT1 is encoded by the SLC6A20
gene. SIT1 is expressed in brain, kidney, small
intestine, thymus, spleen, ovary, and lung. SLC6A20 is a
candidate gene for the rare disorder iminoglycinuria.
This subgroup belongs to the solute carrier 6 (SLC6)
transporter family.
Length = 576
Score = 25.6 bits (56), Expect = 6.4
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 84 INKNNS--VKDCEQKRAGQYFFYEE 106
+N N + ++CE+ QYF+Y E
Sbjct: 127 LNSNRTGYTEECEKASPTQYFWYRE 151
>gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM
protein HpnJ. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The member of this clade
from Acidithiobacillus ferrooxidans ATCC 23270
(AFE_0975) is found in the same locus as squalene-hopene
cyclase (SHC, TIGR01507) and other genes associated with
the biosynthesis of hopanoid natural products.
Similarly, in Ralstonia eutropha JMP134 (Reut_B4901)
this gene is adjacent to HpnAB, IspH and HpnH
(TIGR03470), although SHC itself is elsewhere in the
genome. Notably, this gene (here named HpnJ) and three
others form a conserved set (HpnIJKL) which occur in a
subset of all genomes containing the SHC enzyme. This
relationship was discerned using the method of partial
phylogenetic profiling. This group includes Zymomonas
mobilis, the organism where the initial hopanoid
biosynthesis locus was described consisting of the genes
HpnA-E and SHC (HpnF). Continuing past SHC are found a
phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and
another radical SAM enzyme (ZMO0874), HpnH. Although
discontinuous in Z. mobilis, we continue the gene symbol
sequence with HpnIJKL. One of the well-described
hopanoid intermediates is bacteriohopanetetrol. In the
conversion from hopene several reactions must occur in
the side chain for which a radical mechanism might be
reasonable. These include the four (presumably
anaerobic) hydroxylations and a methyl shift.
Length = 472
Score = 25.4 bits (56), Expect = 7.1
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 6 LTLQVIKRFILHAKKTGFVVEHDFIM 31
LT+++ +RF K G V FI+
Sbjct: 320 LTVEIARRFTRDCHKLGIKVHGTFIL 345
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance to
organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 25.2 bits (56), Expect = 7.3
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 11/52 (21%)
Query: 7 TLQVIKRFILHAKK----TGFVVEHDFIMATYLSDRV-------IVFEGSPS 47
+ VI I T +V HD ++DRV ++ EG+P
Sbjct: 180 SAGVIDELIRELNDALGLTVIMVTHDLDSLLTIADRVAVLADGKVIAEGTPE 231
>gnl|CDD|172732 PRK14244, PRK14244, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 25.2 bits (55), Expect = 8.2
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 10 VIKRFILHAKK--TGFVVEHDFIMATYLSDRVIVFEG 44
VI+ I KK T VV H A +SDRV F+
Sbjct: 187 VIENLIQELKKNFTIIVVTHSMKQAKKVSDRVAFFQS 223
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of the
carbohydrate and solute transporters-like. This family
is comprised of proteins involved in the transport of
apparently unrelated solutes and proteins specific for
di- and oligosaccharides and polyols. ABC transporters
are a large family of proteins involved in the transport
of a wide variety of different compounds, like sugars,
ions, peptides and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 213
Score = 24.8 bits (55), Expect = 8.7
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 11 IKRFILHAKKTGFVVEHDFIMATYLSDRVIV 41
+K T V HD A L+DR+ V
Sbjct: 173 LKELQRELGITTIYVTHDQEEALALADRIAV 203
>gnl|CDD|239850 cd04385, RhoGAP_ARAP, RhoGAP_ARAP: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain
present in ARAPs. ARAPs (also known as centaurin
deltas) contain, besides the RhoGAP domain, an Arf GAP,
ankyrin repeat ras-associating, and PH domains. Since
their ArfGAP activity is PIP3-dependent, ARAPs are
considered integration points for phosphoinositide, Arf
and Rho signaling. Small GTPases cluster into distinct
families, and all act as molecular switches, active in
their GTP-bound form but inactive when GDP-bound. The
Rho family of GTPases activates effectors involved in a
wide variety of developmental processes, including
regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 184
Score = 25.0 bits (55), Expect = 9.8
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 59 LNGMNKFLSLLGITFRRDPNNFRPRINKNN 88
NG N + L FR+D + + R +
Sbjct: 39 KNGKNSSVKKLLEAFRKDARSVQLREGEYT 68
>gnl|CDD|227634 COG5324, COG5324, Uncharacterized conserved protein [Function
unknown].
Length = 758
Score = 24.9 bits (54), Expect = 10.0
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 8 LQVIKRFILHAKKTGFVVEHDFIMATYLSDRVIVFEGSPSISTLANAPQNLLNGMNKFLS 67
+V K+ I KK + ++ + A Y++ F+ L + + +++ ++FL
Sbjct: 296 REVTKQPI-SGKKPSYT-KYKKVTAEYITFCDKKFKEDEDAKRLYMSNKGIISLRDEFLV 353
Query: 68 LLGI 71
L +
Sbjct: 354 LSKL 357
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
0.325 0.140 0.417
Gapped
Lambda K H
0.267 0.0633 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,469,719
Number of extensions: 464682
Number of successful extensions: 568
Number of sequences better than 10.0: 1
Number of HSP's gapped: 568
Number of HSP's successfully gapped: 49
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)