RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18174
(144 letters)
>gnl|CDD|238723 cd01446, DSP_MapKP, N-terminal regulatory rhodanese domain of dual
specificity phosphatases (DSP), such as Mapk
Phosphatase. This domain is believed to determine
substrate specificity by binding the substrate, such as
ERK2, and activating the C-terminal catalytic domain by
inducing a conformational change. This domain has
homology to the Rhodanese Homology Domain.
Length = 132
Score = 93.5 bits (233), Expect = 2e-25
Identities = 45/123 (36%), Positives = 63/123 (51%), Gaps = 10/123 (8%)
Query: 18 SKSWLLQELRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIK 77
+WL LR RL++LDCR EY+ SHIR AVN P+I+ RRL GKI L +
Sbjct: 3 DCAWLAALLREGGERLLLLDCRPFLEYSSSHIRGAVNVCCPTILRRRLQGGKILLQQLLS 62
Query: 78 CRELKEKIMNAYKDSLFVVYGDSCMSEVEVRDREKHCYTASDTMNVLTK--RLQQDGCQV 135
C E ++++ ++ VVY +S +R+ S +VL K R Q+GC V
Sbjct: 63 CPEDRDRLRRGESLAV-VVYDESSSDRERLRE-------DSTAESVLGKLLRKLQEGCSV 114
Query: 136 VCL 138
L
Sbjct: 115 YLL 117
>gnl|CDD|216005 pfam00581, Rhodanese, Rhodanese-like domain. Rhodanese has an
internal duplication. This Pfam represents a single copy
of this duplicated domain. The domain is found as a
single copy in other proteins, including phosphatases
and ubiquitin C-terminal hydrolases.
Length = 106
Score = 51.4 bits (123), Expect = 2e-09
Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 14/86 (16%)
Query: 18 SKSWLLQELRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIK 77
+ L L +D ++++D RS EY + HI AVN + L +L
Sbjct: 1 TAEELKALLEAD--DVVLIDVRSPEEYAKGHIPGAVNIPLSLPSLDKLE----------- 47
Query: 78 CRELKEKIMNAYKDSLFVVYGDSCMS 103
EL+E KD VVY S
Sbjct: 48 -SELEELGKKLDKDKTIVVYCASGNR 72
>gnl|CDD|197731 smart00450, RHOD, Rhodanese Homology Domain. An alpha beta fold
found duplicated in the Rhodanese protein. The the
Cysteine containing enzymatically active version of the
domain is also found in the CDC25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and stress proteins such as Senesence
specific protein 1 in plants, PspE and GlpE in bacteria
and cyanide and arsenate resistance proteins. Inactive
versions with a loss of the cysteine are also seen in
Dual specificity phosphatases, ubiquitin hydrolases from
yeast and in sulfuryltransferases. These are likely to
play a role in protein interactions.
Length = 100
Score = 46.3 bits (110), Expect = 2e-07
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 32 RLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIKCRELKEKIMNAYKD 91
++++LD RS EY HI AVN + ++ RR +E +K L KD
Sbjct: 4 KVVLLDVRSPEEYEGGHIPGAVNIPLSELLDRRGELDILEFEELLKRLGLD-------KD 56
Query: 92 SLFVVYGDS 100
VVY S
Sbjct: 57 KPVVVYCRS 65
>gnl|CDD|238725 cd01448, TST_Repeat_1, Thiosulfate sulfurtransferase (TST),
N-terminal, inactive domain. TST contains 2 copies of
the Rhodanese Homology Domain; this is the 1st repeat,
which does not contain the catalytically active Cys
residue. The role of the 1st repeat is uncertain, but it
is believed to be involved in protein interaction.
Length = 122
Score = 43.4 bits (103), Expect = 3e-06
Identities = 26/96 (27%), Positives = 34/96 (35%), Gaps = 17/96 (17%)
Query: 17 VSKSWLLQELRSDPSRLIILDCRSS-------NEYTESHIRHAVNFSIPSIMLRRLAAGK 69
VS WL + L DP + ILD R EY E HI AV F + K
Sbjct: 2 VSPDWLAEHL-DDP-DVRILDARWYLPDRDGRKEYLEGHIPGAVFFDL-----DEDLDDK 54
Query: 70 IELLSTIKCRELKEKIMNAY---KDSLFVVYGDSCM 102
+ E +++ + D VVY D
Sbjct: 55 SPGPHMLPSPEEFAELLGSLGISNDDTVVVYDDGGG 90
>gnl|CDD|238089 cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold
domain found duplicated in the rhodanese protein. The
cysteine containing enzymatically active version of the
domain is also found in the Cdc25 class of protein
phosphatases and a variety of proteins such as sulfide
dehydrogenases and certain stress proteins such as
senesence specific protein 1 in plants, PspE and GlpE in
bacteria and cyanide and arsenate resistance proteins.
Inactive versions (no active site cysteine) are also
seen in dual specificity phosphatases, ubiquitin
hydrolases from yeast and in sulfuryltransferases, where
they are believed to play a regulatory role in
multidomain proteins.
Length = 89
Score = 36.5 bits (85), Expect = 6e-04
Identities = 17/74 (22%), Positives = 22/74 (29%), Gaps = 19/74 (25%)
Query: 29 DPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIKCRELKEKIMNA 88
D ++LD R EY HI A+N + + R
Sbjct: 7 DDEDAVLLDVREPEEYAAGHIPGAINIPLSELEERAALLEL------------------- 47
Query: 89 YKDSLFVVYGDSCM 102
KD VVY S
Sbjct: 48 DKDKPIVVYCRSGN 61
>gnl|CDD|238783 cd01525, RHOD_Kc, Member of the Rhodanese Homology Domain
superfamily. Included in this CD are the rhodanese-like
domains found C-terminal of the serine/threonine protein
kinases catalytic (S_TKc) domain and the Tre-2, BUB2p,
Cdc16p (TBC) domain. The putative active site Cys
residue is not present in this CD.
Length = 105
Score = 36.7 bits (85), Expect = 6e-04
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 10/81 (12%)
Query: 26 LRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIKCRELKEKI 85
L + P++L +D RSS ++ HI ++N S+ L G++E L T+
Sbjct: 10 LDNSPAKLAAVDIRSSPDFRRGHIEGSINIPFSSVF---LKEGELEQLPTV-------PR 59
Query: 86 MNAYKDSLFVVYGDSCMSEVE 106
+ YK + V+ S
Sbjct: 60 LENYKGKIIVIVSHSHKHAAL 80
>gnl|CDD|238788 cd01530, Cdc25, Cdc25 phosphatases are members of the Rhodanese
Homology Domain superfamily. They activate the cell
division kinases throughout the cell cycle progression.
Cdc25 phosphatases dephosphorylate phosphotyrosine and
phosphothreonine residues, in order to activate their
Cdk/cyclin substrates. Cdc25A phosphatase functions to
regulate S phase entry and Cdc25B is required for G2/M
phase transition of the cell cycle. The Cdc25 domain
binds oxyanions at the catalytic site and has the
signature motif (H/YCxxxxxR).
Length = 121
Score = 33.7 bits (78), Expect = 0.011
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 33 LIILDCRSSNEYTESHIRHAVNFS 56
II+DCR EY HI+ AVN S
Sbjct: 24 YIIIDCRFPYEYNGGHIKGAVNLS 47
>gnl|CDD|225450 COG2897, SseA, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 285
Score = 33.5 bits (77), Expect = 0.021
Identities = 30/109 (27%), Positives = 40/109 (36%), Gaps = 21/109 (19%)
Query: 1 MKMPAGEEEFTTLELCVSKSWLLQELRSDPSRLIILDCR-------SSNEYTESHIRHAV 53
M + A + E VS WL + L D ++I+D R + EY E HI AV
Sbjct: 1 MSLSAL----MSSEFLVSPDWLAENL--DDPAVVIVDARIILPDPDDAEEYLEGHIPGAV 54
Query: 54 NFSIPSIMLRRLAAGKIELLSTIKCRELKEKIMNAY---KDSLFVVYGD 99
F + L L S E K++ D VVY D
Sbjct: 55 FFDWEAD-LSDPVPLPHMLPSP----EQFAKLLGELGIRNDDTVVVYDD 98
>gnl|CDD|104071 PRK09629, PRK09629, bifunctional thiosulfate
sulfurtransferase/phosphatidylserine decarboxylase;
Provisional.
Length = 610
Score = 32.0 bits (72), Expect = 0.10
Identities = 31/94 (32%), Positives = 44/94 (46%), Gaps = 12/94 (12%)
Query: 10 FTTLELCVSKSWLLQELRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGK 69
FT L L + + LL+ L D LI++D SS Y HIR A F P +R GK
Sbjct: 4 FTGLSLVIEPNDLLERL--DAPELILVDLTSSARYEAGHIRGA-RFVDP----KRTQLGK 56
Query: 70 IE----LLSTIKCRELKEKIMNAYKDSLFVVYGD 99
L T +L ++ + D+++VVY D
Sbjct: 57 PPAPGLLPDTADLEQLFGELGHN-PDAVYVVYDD 89
>gnl|CDD|238782 cd01524, RHOD_Pyr_redox, Member of the Rhodanese Homology Domain
superfamily. Included in this CD are the Lactococcus
lactis NADH oxidase, Bacillus cereus NADH
dehydrogenase, and Bacteroides thetaiotaomicron
pyridine nucleotide-disulphide oxidoreductase, and
similar rhodanese-like domains found C-terminal of the
pyridine nucleotide-disulphide oxidoreductase
(Pyr-redox) domain and the Pyr-redox dimerization
domain.
Length = 90
Score = 29.5 bits (67), Expect = 0.19
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 25 ELR-SDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLR-RLA 66
EL + ++D R+ E+ + HI+ A+N IP LR RL
Sbjct: 5 ELDNYRADGVTLIDVRTPQEFEKGHIKGAIN--IPLDELRDRLN 46
>gnl|CDD|238779 cd01521, RHOD_PspE2, Member of the Rhodanese Homology Domain
superfamily. This CD includes the putative
rhodanese-like protein, Psp2, of Yersinia pestis biovar
Medievalis and other similar uncharacterized proteins.
Length = 110
Score = 30.0 bits (68), Expect = 0.20
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 20/75 (26%)
Query: 26 LRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELLSTIKCRELKEKI 85
L++ +++D RS+ Y H+ A+N +P R + L
Sbjct: 19 LKNGKPDFVLVDVRSAEAYARGHVPGAIN--LPH---REICENATAKLD----------- 62
Query: 86 MNAYKDSLFVVYGDS 100
K+ LFVVY D
Sbjct: 63 ----KEKLFVVYCDG 73
>gnl|CDD|227436 COG5105, MIH1, Mitotic inducer, protein phosphatase [Cell division
and chromosome partitioning].
Length = 427
Score = 30.4 bits (68), Expect = 0.29
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 34 IILDCRSSNEYTESHIRHAVNFS 56
II+DCR EY HI +AVN S
Sbjct: 265 IIIDCRFEYEYRGGHIINAVNIS 287
>gnl|CDD|148738 pfam07302, AroM, AroM protein. This family consists of several
bacterial and archaeal AroM proteins. In Escherichia
coli the aroM gene is cotranscribed with aroL. The
function of this family is unknown.
Length = 221
Score = 28.8 bits (65), Expect = 0.76
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 9/55 (16%)
Query: 24 QELRSDPSRLIILDCRSSNEYTESH---IRHAVNFSIPSIMLRRLAAGKI-ELLS 74
+EL + LI+LDC YT++ ++ A+ P ++ R L A ELLS
Sbjct: 172 RELLDQGADLIVLDCIG---YTQAMKDMLQEALG--KPVLLSRVLVARLAAELLS 221
>gnl|CDD|223680 COG0607, PspE, Rhodanese-related sulfurtransferase [Inorganic ion
transport and metabolism].
Length = 110
Score = 28.4 bits (63), Expect = 0.81
Identities = 10/36 (27%), Positives = 13/36 (36%)
Query: 17 VSKSWLLQELRSDPSRLIILDCRSSNEYTESHIRHA 52
+ S L ++LD R EY HI A
Sbjct: 5 ETISEDEAALLLAGEDAVLLDVREPEEYERGHIPGA 40
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B. This region of DNA
polymerase B appears to consist of more than one
structural domain, possibly including elongation,
DNA-binding and dNTP binding activities.
Length = 458
Score = 28.8 bits (65), Expect = 1.1
Identities = 10/50 (20%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 82 KEKIMNAYKDSLFVVYG--DSCMSEVEVRDREKHCYTASDTMNVLTKRLQ 129
K + V+YG DS + D E+ + +T L
Sbjct: 198 KRYVEELLNYGFKVIYGDTDSVFVKFPGVDIEEAKKLGKELAKHVTSELF 247
>gnl|CDD|238778 cd01520, RHOD_YbbB, Member of the Rhodanese Homology Domain
superfamily. This CD includes several putative ATP /GTP
binding proteins including E. coli YbbB.
Length = 128
Score = 27.6 bits (62), Expect = 1.3
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 13/74 (17%)
Query: 32 RLIILDCRSSNEYTESHIRHAVNFSIPSIM-LRRLAAGK----------IELLSTIKCRE 80
++D RS E+ E H+ A+N +P + R G IEL + +
Sbjct: 13 DGPLIDVRSPKEFFEGHLPGAIN--LPLLDDEERALVGTLYKQQGREAAIELGLELVSGK 70
Query: 81 LKEKIMNAYKDSLF 94
LK + A++ L
Sbjct: 71 LKRILNEAWEARLE 84
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine
synthase, essential for modification of some tRNAs to
replace a sulfur atom with selenium. This enzyme works
with SelD, the selenium donor protein, which also acts
in selenocysteine incorporation. Although the members
of this protein family show a fairly deep split,
sequences from both sides of the split are supported by
co-occurence with, and often proximity to, the selD
gene [Protein synthesis, tRNA and rRNA base
modification].
Length = 311
Score = 27.9 bits (63), Expect = 1.7
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 35 ILDCRSSNEYTESHIRHAVNF 55
++D RS E+ E H+ A+N
Sbjct: 5 LIDVRSPAEFAEGHLPGAINL 25
>gnl|CDD|112624 pfam03820, Mtc, Tricarboxylate carrier.
Length = 307
Score = 27.7 bits (62), Expect = 2.1
Identities = 8/35 (22%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 110 REKHCYTASDTMNVLTKRLQQDGCQVVCLLVLKYR 144
R +H + ++ +N+L+ Q + + +V +YR
Sbjct: 9 RARHFFEITNPLNLLSSEKQLEKAR---KIVERYR 40
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 27.5 bits (62), Expect = 2.9
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 35 ILDCRSSNEYTESHIRHAVNF 55
++D RS E+ E HI A+N
Sbjct: 18 LIDVRSPIEFAEGHIPGAINL 38
>gnl|CDD|238784 cd01526, RHOD_ThiF, Member of the Rhodanese Homology Domain
superfamily. This CD includes several putative
molybdopterin synthase sulfurylases including the
molybdenum cofactor biosynthetic protein (CnxF) of
Aspergillus nidulans and the molybdenum cofactor
synthesis protein 3 (MOCS3) of Homo sapiens. These
rhodanese-like domains are found C-terminal of the ThiF
and MoeZ_MoeB domains.
Length = 122
Score = 26.5 bits (59), Expect = 3.0
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 23 LQELRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELL 73
+ + + ++LD R + + A+N IP L AA L
Sbjct: 15 YKNILQAGKKHVLLDVRPKVHFEICRLPEAIN--IPLSELLSKAAELKSLQ 63
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 27.2 bits (61), Expect = 4.0
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 16/77 (20%)
Query: 14 ELCVSKSWLLQELRSDPSRLIILDCRSSNEYTESHIRHAVNFSIPSIMLRRLAAGKIELL 73
ELC Q L+ +P +I+ +EY I + P + LR +
Sbjct: 265 ELC------RQILKFNPKEIILFS---RDEYKLYLIDMELREKFPELKLRF-------YI 308
Query: 74 STIKCRELKEKIMNAYK 90
++ R+ E+ M +K
Sbjct: 309 GDVRDRDRVERAMEGHK 325
>gnl|CDD|213953 TIGR04340, rSAM_ACGX, radical SAM/SPASM domain protein, ACGX
system. Members of this protein family are radical
SAM/SPASM domain proteins likely to be involved in the
modification of small, Cys-rich peptides. Members of the
family of proposed target sequences, TIGR04341, average
75 amino acids in length and average six instances of
the motif ACGX, where X is A, S, or T.
Length = 341
Score = 26.7 bits (59), Expect = 4.4
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 78 CRELKEKIMNAYKDSLFVVYGDSCMSEVEVRDREKHCYT 116
CR + K+ NA D L+ V+ + M + D+ + C
Sbjct: 271 CRRFESKVGNALTDRLYDVFLGNEMDKYRQIDKFEKCSR 309
>gnl|CDD|107346 cd06351, PBP1_iGluR_N_LIVBP_like, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the NMDA, AMPA, and kainate receptor subtypes
of ionotropic glutamate receptors (iGluRs). While this
N-terminal domain belongs to the periplasmic-binding
fold type I superfamily, the glutamate-binding domain of
the iGluR is structurally homologous to the
periplasmic-binding fold type II. The LIVBP-like domain
of iGluRs is thought to play a role in the initial
assembly of iGluR subunits, but it is not well
understood how this domain is arranged and functions in
intact iGluR. Glutamate mediates the majority of
excitatory synaptic transmission in the central nervous
system via two broad classes of ionotropic receptors
characterized by their response to glutamate agonists:
N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA
receptors have intrinsically slow kinetics, are highly
permeable to Ca2+, and are blocked by extracellular Mg2+
in a voltage-dependent manner. On the other hand,
non-NMDA receptors have faster kinetics, are weakly
permeable to Ca2+, and are not blocked by extracellular
Mg2+. While non-NMDA receptors typically mediate
excitatory synaptic responses at resting membrane
potentials, NMDA receptors contribute to several forms
of synaptic plasticity and are suggested to play an
important role in the development of synaptic pathways.
Length = 328
Score = 26.3 bits (58), Expect = 6.1
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 22 LLQELRSDPSRLIILDCRSSNEYTE 46
LL+EL+ SR IILDC S E E
Sbjct: 177 LLKELKRSESRRIILDCSSEEEAKE 201
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
0.322 0.134 0.390
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,057,811
Number of extensions: 610063
Number of successful extensions: 526
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 31
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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 (21.9 bits)
S2: 54 (24.8 bits)