RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8943
(134 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 101 bits (254), Expect = 5e-26
Identities = 37/83 (44%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 6 TIRRGSRCSTSKAFLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHII 65
T+ G R S ++A+L P R NL I R+LF+ +AVG+E R G +
Sbjct: 193 TVTNGRRWSAARAYLDPALKRPNLTIVTHALTDRILFEG----KRAVGVEYERGGGRETA 248
Query: 66 RAKKEIISSAGAINSPQLLMVSG 88
RA++E+I SAGAINSPQLL +SG
Sbjct: 249 RARREVILSAGAINSPQLLQLSG 271
Score = 79.1 bits (196), Expect = 3e-18
Identities = 28/46 (60%), Positives = 32/46 (69%), Gaps = 1/46 (2%)
Query: 86 VSGGSSVLNAMIYVRGNKNDYDQW-ERLGNSGWGYKDVLPYFKKSE 130
V GGSS +N M+Y+RGN DYD W E G GW Y D LPYFKK+E
Sbjct: 87 VLGGSSSINGMVYIRGNAMDYDNWAELPGLEGWSYADCLPYFKKAE 132
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 82.5 bits (204), Expect = 2e-19
Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 6/87 (6%)
Query: 4 QGTIRRGSRCSTSKAFLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRD--GR 61
TI G R S ++A+L+P R NL + + R+L + +AVG+E+ G
Sbjct: 193 CVTICNGRRWSAARAYLKPALKRPNLTLLTGARVRRILLEGD----RAVGVEVEIGDGGT 248
Query: 62 KHIIRAKKEIISSAGAINSPQLLMVSG 88
A +E++ +AGAINSP+LL++SG
Sbjct: 249 IETAVAAREVVLAAGAINSPKLLLLSG 275
Score = 73.6 bits (181), Expect = 2e-16
Identities = 26/46 (56%), Positives = 33/46 (71%), Gaps = 1/46 (2%)
Query: 88 GGSSVLNAMIYVRGNKNDYDQW-ERLGNSGWGYKDVLPYFKKSEDN 132
GGSS +N M+YVRG+ D+D W + G GW Y DVLPYFK++ED
Sbjct: 88 GGSSSINGMVYVRGHPEDFDAWAQESGAPGWPYDDVLPYFKRAEDL 133
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 78.0 bits (192), Expect = 8e-18
Identities = 34/83 (40%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 6 TIRRGSRCSTSKAFLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHII 65
T+ G R S ++A+L P R NL + ++ F+ + +A G+E + GRK
Sbjct: 186 TVHNGRRVSAARAYLHPAMKRPNLEVQTRAFVTKINFEGN----RATGVEFKKGGRKEHT 241
Query: 66 RAKKEIISSAGAINSPQLLMVSG 88
A KE+I SAGAINSPQLL +SG
Sbjct: 242 EANKEVILSAGAINSPQLLQLSG 264
Score = 65.3 bits (159), Expect = 2e-13
Identities = 24/46 (52%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 86 VSGGSSVLNAMIYVRGNKNDYDQWER-LGNSGWGYKDVLPYFKKSE 130
V GGSS +N MIY RGN DY++W + G W Y D LPY+K+ E
Sbjct: 81 VLGGSSSINGMIYQRGNPMDYEKWAKPEGMESWDYADCLPYYKRLE 126
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 68.8 bits (169), Expect = 3e-15
Identities = 31/83 (37%), Positives = 50/83 (60%), Gaps = 5/83 (6%)
Query: 8 RRGSRCSTSKAFLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRD--GRKHII 65
G++ ST++ +LRP L +NL I +A +++ G +AVG+E G K +I
Sbjct: 122 PTGAKQSTARTWLRPA-LERNLRILTGAKAEKIIILGRGG--RAVGVEARDGGGGIKRLI 178
Query: 66 RAKKEIISSAGAINSPQLLMVSG 88
A KE++ +AGA+N+P LL+ SG
Sbjct: 179 TAAKEVVVAAGALNTPPLLLRSG 201
Score = 61.5 bits (150), Expect = 1e-12
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 74 SAGAINSPQLLMVS----GGSSVLNAMIYVRGNKNDYDQWERL-GNSGWGYKDVLPYFKK 128
SAG++N ++++ + GG S +N +R D+W G GWGY D LPY K
Sbjct: 10 SAGSVNGRRMILPAGSTVGGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDK 69
Query: 129 SE 130
E
Sbjct: 70 VE 71
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 65.6 bits (160), Expect = 2e-13
Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 5/79 (6%)
Query: 10 GSRCSTSKAFLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKK 69
G R ST+ A+L P R NL + +T+ +R+LF + +AVG+E+L DG +RA +
Sbjct: 191 GRRVSTAVAYLLPALKRPNLTVEADTRVVRILFSGT----RAVGVEVLGDGGPRTLRADR 246
Query: 70 EIISSAGAINSPQLLMVSG 88
++ AGA+ S LL++SG
Sbjct: 247 -VVLCAGAVESAHLLLLSG 264
Score = 49.0 bits (117), Expect = 9e-08
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 86 VSGGSSVLNAMIYVRGNKNDYDQWERLGNSGWGYKDVLPYFKKSEDNRN 134
V GGS +N + R D+D W GW + DVLP+F+ E + +
Sbjct: 83 VLGGSGAVNGGYFCRALPADFDAWPI---PGWSWDDVLPHFRAIETDLD 128
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 50.2 bits (120), Expect = 4e-08
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 7/68 (10%)
Query: 27 KNLHIAMETQALRLLFDKSGPVPKAVGIEILRD--GRKHII----RAKKEIISSAGAINS 80
L + + +++FD SG P+A G+ I +D G +H EII SAGAI S
Sbjct: 233 NKLRVLLHATVQKIVFDTSGKRPRATGV-IFKDENGNQHQAFLSNNKGSEIILSAGAIGS 291
Query: 81 PQLLMVSG 88
PQ+L++SG
Sbjct: 292 PQMLLLSG 299
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 37.9 bits (89), Expect = 6e-04
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 25 LRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAG 76
+ I +T+A RL+ D G V VG+E R G IRA+K ++ +AG
Sbjct: 188 AALGVQIRYDTRATRLIVDDDGRV---VGVEARRYGETVAIRARKGVVLAAG 236
>gnl|CDD|235758 PRK06263, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 543
Score = 36.1 bits (84), Expect = 0.002
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 26 RKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAGA 77
++ + I E A++L+ D++ V A+ ++ LR+G I AK I+++ GA
Sbjct: 146 KERIKILEEVMAIKLIVDENREVIGAIFLD-LRNGEIFPIYAKATILATGGA 196
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 34.6 bits (80), Expect = 0.008
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 26 RKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAGA 77
+ I E L LL D G V V + LR G ++ RAK I+++ GA
Sbjct: 151 FSGIEIFDEYFVLDLLVDDGGGVAGVVARD-LRTGELYVFRAKAVILATGGA 201
>gnl|CDD|233702 TIGR02061, aprA, adenosine phosphosulphate reductase, alpha
subunit. During dissimilatory sulfate reduction or
sulfur oxidation, adenylylsulfate (APS) reductase
catalyzes reversibly the two-electron reduction of APS
to sulfite and AMP. Found in several bacterial lineages
and in Archaeoglobales, APS reductase is a heterodimer
composed of an alpha subunit containing a noncovalently
bound FAD, and a beta subunit containing two [4Fe-4S]
clusters. Described by this model is the alpha subunit
of APS reductase, sharing common evolutionary origin
with fumarate reductase/succinate dehydrogenase
flavoproteins [Central intermediary metabolism, Sulfur
metabolism].
Length = 614
Score = 32.2 bits (73), Expect = 0.061
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 39 RLLFDKSGP--VPKAVGIEILRDGRKHIIRAKKEIISSAGAIN 79
+LL DK+ P + AVG +R H+ +AK I+++ GA+N
Sbjct: 151 KLLLDKNTPNRIAGAVGFN-VRANEVHVFKAKTVIVAAGGAVN 192
>gnl|CDD|219550 pfam07745, Glyco_hydro_53, Glycosyl hydrolase family 53. This
domain belongs to family 53 of the glycosyl hydrolase
classification. These enzymes are enzymes are endo-1,4-
beta-galactanases (EC:3.2.1.89). The structure of this
domain is known and has a TIM barrel fold.
Length = 332
Score = 31.2 bits (71), Expect = 0.13
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 85 MVSGGSSVLNAMIYVRGNKNDYDQWERLGNSG-WGYKDVLP 124
MV G+ + + M++ G +++ +L NSG W KDV P
Sbjct: 128 MVQVGNEITSGMLWPEGKTPNWENIAKLLNSGYWAVKDVNP 168
>gnl|CDD|237221 PRK12835, PRK12835, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 584
Score = 28.6 bits (64), Expect = 1.1
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 33 METQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAG 76
+++ L+ D G V VG + R+GR I A++ +I + G
Sbjct: 232 LDSPMTELITDPDGAV---VGAVVEREGRTLRIGARRGVILATG 272
>gnl|CDD|233582 TIGR01812, sdhA_frdA_Gneg, succinate dehydrogenase or fumarate
reductase, flavoprotein
subunitGram-negative/mitochondrial subgroup. This model
represents the succinate dehydrogenase flavoprotein
subunit as found in Gram-negative bacteria,
mitochondria, and some Archaea. Mitochondrial forms
interact with ubiquinone and are designated EC 1.3.5.1,
but can be degraded to 1.3.99.1. Some isozymes in E.
coli and other species run primarily in the opposite
direction and are designated fumarate reductase [Energy
metabolism, Aerobic, Energy metabolism, Anaerobic,
Energy metabolism, TCA cycle].
Length = 541
Score = 27.7 bits (62), Expect = 1.8
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 25 LRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAGA 77
L+ + E AL L+ D + V L+ G RAK ++++ G
Sbjct: 117 LKLGVSFFNEYFALDLIHD--DGRVRGVVAYDLKTGEIVFFRAKAVVLATGGY 167
>gnl|CDD|226385 COG3867, COG3867, Arabinogalactan endo-1,4-beta-galactosidase
[Carbohydrate transport and metabolism].
Length = 403
Score = 27.1 bits (60), Expect = 3.1
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 85 MVSGGSSVLNAMIYVRGNKNDYDQWERLGNSGWG 118
MV G+ ++ G ++D+ L N+G
Sbjct: 174 MVQVGNETNGGFLWPDGEGRNFDKMAALLNAGIR 207
>gnl|CDD|235879 PRK06854, PRK06854, adenylylsulfate reductase subunit alpha;
Validated.
Length = 608
Score = 26.8 bits (60), Expect = 3.8
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 51 AVGIEILRDGRKHIIRAKKEIISSAGAIN 79
AVG + R+ + ++ +AK I+++ GA
Sbjct: 169 AVGFSV-RENKFYVFKAKAVIVATGGAAG 196
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 26.9 bits (60), Expect = 4.0
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 34 ETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAGAI-NSPQLLMVSGGSSV 92
A L+ + G V V +E R+GR+ IRA ++ + G + +LL+ + G +
Sbjct: 160 RHPADDLIVE-DGRVTGVV-VENRRNGREVRIRAIAGVLLATGGFGRNAELLLPAAGYAD 217
Query: 93 LNAMIYVRGN 102
G+
Sbjct: 218 TTGPPANTGD 227
>gnl|CDD|233850 TIGR02402, trehalose_TreZ, malto-oligosyltrehalose
trehalohydrolase. Members of this family are the
trehalose biosynthetic enzyme malto-oligosyltrehalose
trehalohydrolase, formally known as
4-alpha-D-{(1->4)-alpha-D-glucano}trehalose
trehalohydrolase (EC 3.2.1.141). It is the TreZ protein
of the TreYZ pathway for trehalose biosynthesis, and
alternative to the OtsAB system [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 544
Score = 26.9 bits (60), Expect = 4.3
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 113 GNSGWGYKDVLPY 125
G GWGY VLPY
Sbjct: 138 GTRGWGYDGVLPY 150
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 25.3 bits (56), Expect = 4.6
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 23 IRLR-KNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGR 61
RLR NLH + + L LF + G V K V I R GR
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKK-VKINYDRSGR 39
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM2 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 73
Score = 25.2 bits (56), Expect = 4.7
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 28 NLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHI 64
NL +E + LR F+ G V + I+RD + I
Sbjct: 6 NLPFDIEEEELRKHFEDCGDV---EAVRIVRDRKTGI 39
>gnl|CDD|238145 cd00236, FinO_conjug_rep, FinO bacterial conjugation repressor
domain; the basic protein FinO is part of the the two
component FinOP system which is responsible for
repressing bacterial conjugation; the FinOP system
represses the transfer (tra) operon of the F-plasmid
which encodes the proteins responsible for conjugative
transfer of this plasmid from host to recipient
Escherichia coli cells; antisense RNA, FinP is thought
to interact with traJ mRNA to occlude its ribosome
binding site, blocking traJ translation and thereby
inhibiting transcription of the tra operon; FinO
protects FinP against degradation by binding to FinP
and sterically blocking the cellular endonuclease RNase
E; FinO also also binds to the complementary stem-loop
structures in traJ mRNA and promotes duplex formation
between FinP and traJ RNA in vitro; this domain
contains two independent RNA binding regions.
Length = 146
Score = 26.0 bits (57), Expect = 5.8
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 39 RLLFDKSGPVPKAVGIE--ILRDGRKH 63
LF P GI+ IL+D +H
Sbjct: 48 PGLFPGDTPRLLKCGIKDGILQDVAQH 74
>gnl|CDD|220075 pfam08928, DUF1910, Domain of unknown function (DUF1910). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 118
Score = 25.4 bits (56), Expect = 6.7
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 3/70 (4%)
Query: 54 IEILRDGRKHIIRAKKEIISSAGAINSPQLLMVSGGSSVLNAMIYVRGNKNDYDQWERLG 113
IE+ D I R +S + SGG S+ Y+ D E +
Sbjct: 29 IELKSDEENGIQRYPNTSLSIFSYNLEILIARYSGGESIEELEAYL---DKLIDYLENIW 85
Query: 114 NSGWGYKDVL 123
+ GY+ +L
Sbjct: 86 DEDDGYQYLL 95
>gnl|CDD|183787 PRK12844, PRK12844, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 26.3 bits (58), Expect = 6.8
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 3 AQGTIRRGSRCSTSKAF---LRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRD 59
IR + A + L + + T L L + G V VG+ ++RD
Sbjct: 194 LAARIRGQKLLTNGAALIGRMLEAALAAGVPLWTNT-PLTELIVEDGRV---VGVVVVRD 249
Query: 60 GRKHIIRAKKEIISSAG 76
GR+ +IRA++ ++ ++G
Sbjct: 250 GREVLIRARRGVLLASG 266
>gnl|CDD|237222 PRK12837, PRK12837, 3-ketosteroid-delta-1-dehydrogenase;
Provisional.
Length = 513
Score = 26.3 bits (58), Expect = 6.9
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 19 FLRPIRLRKNLHIAMETQALRLLFDKSGPVPKAVGIEILRDGRKHIIRAKKEIISSAG 76
FL + N + + T L L + G V VG + R G + +RA++ ++ +AG
Sbjct: 179 FLAALARFPNARLRLNT-PLVELVVEDGRV---VGAVVERGGERRRVRARRGVLLAAG 232
>gnl|CDD|239310 cd03012, TlpA_like_DipZ_like, TlpA-like family, DipZ-like
subfamily; composed uncharacterized proteins containing
a TlpA-like TRX domain. Some members show domain
architectures similar to that of E. coli DipZ protein
(also known as DsbD). The only eukaryotic members of the
TlpA family belong to this subfamily. TlpA is a
disulfide reductase known to have a crucial role in the
biogenesis of cytochrome aa3.
Length = 126
Score = 25.3 bits (56), Expect = 7.9
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 102 NKNDYDQWERLGNSGW 117
N NDY W GN W
Sbjct: 91 NDNDYATWRAYGNQYW 106
>gnl|CDD|240167 cd05144, RIO2_C, RIO kinase family; RIO2, C-terminal catalytic
domain. The RIO kinase catalytic domain family is part
of a larger superfamily, that includes the catalytic
domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase (PI3K). RIO kinases are
atypical protein serine kinases containing a kinase
catalytic signature, but otherwise show very little
sequence similarity to typical PKs. Serine kinases
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine residues in protein substrates. The RIO
catalytic domain is truncated compared to the catalytic
domains of typical PKs, with deletions of the loops
responsible for substrate binding. RIO2 is present in
archaea and eukaryotes. It contains an N-terminal winged
helix (wHTH) domain and a C-terminal RIO kinase
catalytic domain. The wHTH domain is primarily seen in
DNA-binding proteins, although some wHTH domains may be
involved in RNA recognition. RIO2 is essential for
survival and is necessary for rRNA cleavage during 40S
ribosomal subunit maturation. The biological substrates
of RIO2 are still unknown.
Length = 198
Score = 25.6 bits (57), Expect = 9.3
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 33 METQALRLLFDKSGPVPKAVGIE 55
E AL+ L+++ PVPK +
Sbjct: 82 KEFAALKALYEEGFPVPKPIDWN 104
>gnl|CDD|233827 TIGR02347, chap_CCT_zeta, T-complex protein 1, zeta subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
zeta chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 531
Score = 25.8 bits (57), Expect = 9.9
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 43 DKSGPVPKAVGIEILRDGRKHI------IRAKKEIISSAGAINSPQLLMV 86
D+ G V + I R KK++I SA I S QLL+V
Sbjct: 472 DEGGE-VVGVDLNTGEPIDPEIKGIWDNYRVKKQLIQSATVIAS-QLLLV 519
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 0.136 0.397
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,882,714
Number of extensions: 612957
Number of successful extensions: 551
Number of sequences better than 10.0: 1
Number of HSP's gapped: 535
Number of HSP's successfully gapped: 39
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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: 54 (24.5 bits)