RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031626
(156 letters)
>gnl|CDD|178408 PLN02812, PLN02812, 5-formyltetrahydrofolate cyclo-ligase.
Length = 211
Score = 196 bits (501), Expect = 8e-65
Identities = 84/132 (63%), Positives = 103/132 (78%), Gaps = 9/132 (6%)
Query: 18 ESIFQQKRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALRE 77
+ I +QK+ LR +VR+ LK++ P R+ ED AIQ +LE PWFKSS+RLCAY+SC+ LRE
Sbjct: 1 DEIREQKKALRKEVRRALKALSPEQRAQEDAAIQSRLLELPWFKSSKRLCAYVSCAKLRE 60
Query: 78 VDTSKLLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSI-DDLIANSMNILEP 136
VDTSK+LS+ILQ P K+LYVPRVEDKNS+MRM HI+ + DDL+ANSMNILEP
Sbjct: 61 VDTSKILSEILQNP--------DKRLYVPRVEDKNSNMRMLHITDMADDLVANSMNILEP 112
Query: 137 APVDADGNERED 148
PVDADGN RED
Sbjct: 113 TPVDADGNPRED 124
>gnl|CDD|233985 TIGR02727, MTHFS_bact, 5,10-methenyltetrahydrofolate synthetase.
This enzyme, 5,10-methenyltetrahydrofolate synthetase,
is also called 5-formyltetrahydrofolate cycloligase.
Function of bacterial proteins in this family was
inferred originally from the known activity of
eukaryotic homologs. Recently, activity was shown
explicitly for the member from Mycoplasma pneumonia.
Members of this family from alpha- and
gamma-proteobacteria, designated ygfA, are often found
in an operon with 6S structural RNA, and show a similar
pattern of high expression during stationary phase. The
function may be to deplete folate to slow 1-carbon
biosynthetic metabolism [Central intermediary
metabolism, One-carbon metabolism].
Length = 179
Score = 67.3 bits (165), Expect = 1e-14
Identities = 32/121 (26%), Positives = 57/121 (47%), Gaps = 14/121 (11%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALR-EVDTSK 82
K+ LR ++ + K++ + R +AI K +L +K+++ + Y+ LR EVDT
Sbjct: 1 KKELRKKLLEARKALSSAERKAASSAIAKRLLALIEWKNAKTIALYLP---LRGEVDTRP 57
Query: 83 LLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSIDD-LIANSMNILEPAPVDA 141
L+ Q+L+ K++ +P+V+ M F I S + L ILEP
Sbjct: 58 LIEQLLKEG---------KRVALPKVDGDGKEMLFFRIWSPEQPLTKGPFGILEPVGDLE 108
Query: 142 D 142
+
Sbjct: 109 E 109
>gnl|CDD|223290 COG0212, COG0212, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme
metabolism].
Length = 191
Score = 56.1 bits (136), Expect = 2e-10
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 11/115 (9%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREVDTSKL 83
K LR + + ++ P R D I K++ K ++ + Y+ + E+DT L
Sbjct: 5 KSALRKLLLERRIALSPEERHEADQRIAKLLASLIEVKKAKTIALYVPFN--GEIDTRPL 62
Query: 84 LSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHISSIDDLIANSMNILEPAP 138
+ Q L+ G K+L +P++ D + + LI N ILEP
Sbjct: 63 IRQALR----RG-----KRLLLPKLRDYKLLFLRYIPDPLQPLIKNRFGILEPGE 108
>gnl|CDD|216717 pfam01812, 5-FTHF_cyc-lig, 5-formyltetrahydrofolate cyclo-ligase
family. 5-formyltetrahydrofolate cyclo-ligase or
methenyl-THF synthetase EC:6.3.3.2 catalyzes the
interchange of 5-formyltetrahydrofolate (5-FTHF) to
5-10-methenyltetrahydrofolate, this requires ATP and
Mg2+. 5-FTHF is used in chemotherapy where it is
clinically known as Leucovorin.
Length = 182
Score = 52.7 bits (127), Expect = 3e-09
Identities = 21/132 (15%), Positives = 51/132 (38%), Gaps = 14/132 (10%)
Query: 24 KRILRSQVRKTLKSMDPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREVDTSKL 83
K+ LR Q+ +++ R+ A+ + + + ++R+ Y+S E+DT +L
Sbjct: 1 KQELRKQLLAKRRALSEEERAAASRALHQKLPSFVGAQKAKRVALYVSVK--GEIDTREL 58
Query: 84 LSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRMFHIS-SIDDLIANSMNILEPAPVDAD 142
+ +L+ K + +PR + + L + + E P++ +
Sbjct: 59 IELLLEE---------GKLVLLPRPRPDSGLVVRITPYYPETGLPSGPYGLPE--PIEEE 107
Query: 143 GNEREDGILLFI 154
E + +
Sbjct: 108 QRELALNQIDLV 119
>gnl|CDD|191103 pfam04821, TIMELESS, Timeless protein. The timeless gene in
Drosophila melanogaster and its homologues in a number
of other insects and mammals (including human) are
involved in circadian rhythm control. This family
includes a related proteins from a number of fungal
species.
Length = 266
Score = 28.4 bits (64), Expect = 1.3
Identities = 29/112 (25%), Positives = 42/112 (37%), Gaps = 38/112 (33%)
Query: 21 FQQKRILRSQVRKTLKSM--DPSLRSHEDNAIQKIVLEAPWFKSSQRLCAYISCSALREV 78
F ++L++ VR L S+ RS DN I +++L
Sbjct: 105 FLDAKVLKALVRILLPSLAVPWEDRSERDNLIIELIL----------------------- 141
Query: 79 DTSKLLSQILQIPNADGDTKTRKKLYVPRVEDKNSHMRM---FHISSIDDLI 127
LL IL IP + + + R ED +SH FH IDDL+
Sbjct: 142 ---LLLRNILHIP-PNPEAEKRGD------EDASSHDATIWAFHQQGIDDLL 183
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 27.6 bits (62), Expect = 2.4
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 120 ISSIDDLIANSMNILEPAPVDA 141
I+SID++ + + I EP VD
Sbjct: 24 ITSIDEIFDSGLPIKEPEIVDV 45
>gnl|CDD|187571 cd05261, CAPF_like_SDR_e, capsular polysaccharide assembling
protein (CAPF) like, extended (e) SDRs. This subgroup
of extended SDRs, includes some members which have been
identified as capsular polysaccharide assembling
proteins, such as Staphylococcus aureus Cap5F which is
involved in the biosynthesis of N-acetyl-l-fucosamine, a
constituent of surface polysaccharide structures of S.
aureus. This subgroup has the characteristic active site
tetrad and NAD-binding motif of extended SDRs. Extended
SDRs are distinct from classical SDRs. In addition to
the Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal extension
of approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 248
Score = 27.7 bits (62), Expect = 2.6
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 105 VPRVEDKNSHMRMFHISSIDDLIANSMNILEPAPVDADG 143
++ D + + + +I DD++ + +LE AP + G
Sbjct: 158 PIQINDPAAELTLVYI---DDVVDELIQLLEGAPTYSGG 193
>gnl|CDD|236406 PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional.
Length = 350
Score = 27.5 bits (62), Expect = 2.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 89 QIPNADGDTKTRKKLYVPRV 108
Q+ N +G+ K KK Y PRV
Sbjct: 304 QVGNPEGEDKPNKKYYDPRV 323
>gnl|CDD|238476 cd00946, FBP_aldolase_IIA, Class II Type A,
Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme
catalyses the zinc-dependent, reversible aldol
condensation of dihydroxyacetone phosphate with
glyceraldehyde-3-phosphate to form
fructose-1,6-bisphosphate. FBP aldolase is homodimeric
and used in gluconeogenesis and glycolysis. The type A
and type B Class II FBPA's differ in the presence and
absence of distinct indels in the sequence that result
in differing loop lengths in the structures.
Length = 345
Score = 26.9 bits (60), Expect = 5.0
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 89 QIPNADGDTKTRKKLYVPRV 108
QI N +G K KK Y PRV
Sbjct: 300 QIGNPEGPDKPNKKYYDPRV 319
>gnl|CDD|236055 PRK07575, PRK07575, dihydroorotase; Provisional.
Length = 438
Score = 26.9 bits (60), Expect = 5.8
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 34 TLKSMDPSLRSHEDNAI 50
TL M+P LRS EDN
Sbjct: 271 TLAQMNPPLRSPEDNEA 287
>gnl|CDD|240658 cd12181, ceo_syn, N(5)-(carboxyethyl)ornithine synthase.
N(5)-(carboxyethyl)ornithine synthase (ceo_syn)
catalyzes the NADP-dependent conversion of
N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine +
pyruvate. Ornithine plays a key role in the urea cycle,
which in mammals is used in arginine biosynthesis, and
is a precursor in polyamine synthesis. ceo_syn is
related to the NAD-dependent L-alanine dehydrogenases.
Like formate dehydrogenase and related enzymes, ceo_syn
is comprised of 2 domains connected by a long alpha
helical stretch, each resembling a Rossmann fold
NAD-binding domain. The NAD-binding domain is inserted
within the linear sequence of the more divergent
catalytic domain. These ceo_syn proteins have a
partially conserved NAD-binding motif and active site
residues that are characteristic of related enzymes such
as Saccharopine Dehydrogenase.
Length = 295
Score = 26.8 bits (60), Expect = 5.9
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 119 HISSIDDLIANSMNILEPAPVDADGNE-REDGIL 151
I S ++++A I +P P DAD E E IL
Sbjct: 55 GIVSREEILAKCDVICDPKPGDADYLEILEGQIL 88
>gnl|CDD|133207 cd05076, PTK_Tyk2_rpt1, Pseudokinase (repeat 1) domain of the
Protein Tyrosine Kinase, Tyrosine kinase 2. Protein
Tyrosine Kinase (PTK) family; Tyrosine kinase 2 (Tyk2);
pseudokinase domain (repeat 1). The PTKc (catalytic
domain) family to which this subfamily belongs, is part
of a larger superfamily that includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Tyk2 is
a member of the Janus kinase (Jak) subfamily of
proteins, which are cytoplasmic (or nonreceptor) tyr
kinases containing an N-terminal FERM domain, followed
by a Src homology 2 (SH2) domain, a pseudokinase
domain, and a C-terminal tyr kinase domain. The
pseudokinase domain shows similarity to tyr kinases but
lacks crucial residues for catalytic activity and ATP
binding. It modulates the kinase activity of the
C-terminal catalytic domain. Jaks are crucial for
cytokine receptor signaling. They are activated by
autophosphorylation upon cytokine-induced receptor
aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs).
Tyk2 is widely expressed in many tissues. It is
involved in signaling via the cytokine receptors
IFN-alphabeta, IL-6, IL-10, IL-12, IL-13, and IL-23. It
mediates cell surface urokinase receptor (uPAR)
signaling and plays a role in modulating vascular
smooth muscle cell (VSMC) functional behavior in
response to injury. Tyk2 is also important in dendritic
cell function and T helper (Th)1 cell differentiation.
A homozygous mutation of Tyk2 was found in a patient
with hyper-IgE syndrome (HIES), a primary
immunodeficiency characterized by recurrent skin
abscesses, pneumonia, and elevated serum IgE. This
suggests that Tyk2 may play important roles in multiple
cytokine signaling involved in innate and adaptive
immunity.
Length = 274
Score = 26.8 bits (59), Expect = 5.9
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 7 SSNPEEKEHDLESIFQQKRILRSQVRKTLKSMDPSLRSHEDNAI 50
PEE E + E + ++R LK +DP SH D A+
Sbjct: 21 GGEPEEDEMEDEDPLVEGNNNGRELRVVLKVLDP---SHRDIAL 61
>gnl|CDD|240198 cd05693, S1_Rrp5_repeat_hs1_sc1, S1_Rrp5_repeat_hs1_sc1: Rrp5 is
a trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
two distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1)
and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 100
Score = 25.3 bits (56), Expect = 8.5
Identities = 10/37 (27%), Positives = 21/37 (56%)
Query: 1 MSQSNDSSNPEEKEHDLESIFQQKRILRSQVRKTLKS 37
+ + ++ + EE+ DLE +F +++R +V KS
Sbjct: 47 LDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS 83
>gnl|CDD|235165 PRK03826, PRK03826, 5'-nucleotidase; Provisional.
Length = 195
Score = 25.7 bits (57), Expect = 8.9
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 12/68 (17%)
Query: 9 NPE-EKE-HDLESIFQQKRILRSQVRKTLKS-MDPSLRSHE-DNAIQKIVLEAPWFKSSQ 64
NPE E +E I +QK L + + L+ P L SH + IV K +
Sbjct: 85 NPEIAHEYKKIEKIAEQK--LLDMLPEELQEDFRPLLDSHAASEEEKAIV------KQAD 136
Query: 65 RLCAYISC 72
LCAY+ C
Sbjct: 137 ALCAYLKC 144
>gnl|CDD|213296 cd05930, A_NRPS, The adenylation domain of nonribosomal peptide
synthetases (NRPS). The adenylation (A) domain of NRPS
recognizes a specific amino acid or hydroxy acid and
activates it as an (amino) acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms a thioester
bond to the enzyme-bound cofactor phosphopantetheine of
a peptidyl carrier protein domain. NRPSs are large
multifunctional enzymes which synthesize many
therapeutically useful peptides in bacteria and fungi
via a template-directed, nucleic acid independent
nonribosomal mechanism. These natural products include
antibiotics, immunosuppressants, plant and animal
toxins, and enzyme inhibitors. NRPS has a distinct
modular structure in which each module is responsible
for the recognition, activation, and in some cases,
modification of a single amino acid residue of the final
peptide product. The modules can be subdivided into
domains that catalyze specific biochemical reactions.
Length = 445
Score = 26.3 bits (59), Expect = 9.3
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 64 QRLCAYISCSALREVDTSKL---LSQIL 88
+RL AY+ +A E+D ++L L++ L
Sbjct: 390 KRLVAYVVPAAGAELDAAELRAFLAERL 417
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
0.315 0.130 0.360
Gapped
Lambda K H
0.267 0.0587 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,588,030
Number of extensions: 649299
Number of successful extensions: 507
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 27
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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: 55 (25.3 bits)