RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5126
(123 letters)
>gnl|CDD|187595 cd05334, DHPR_SDR_c_like, dihydropteridine reductase (DHPR),
classical (c) SDRs. Dihydropteridine reductase is an
NAD-binding protein related to the SDRs. It converts
dihydrobiopterin into tetrahydrobiopterin, a cofactor
necessary in catecholamines synthesis. Dihydropteridine
reductase has the YXXXK of these tyrosine-dependent
oxidoreductases, but lacks the typical upstream Asn and
Ser catalytic residues. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H)-binding pattern (typically, TGxxxGxG in
classical SDRs and TGxxGxxG in extended SDRs), while
substrate binding is in the C-terminal region. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK pattern.
In addition to the Tyr and Lys, there is often an
upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn
(Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and aromatic
compounds. The standard reaction mechanism is a proton
relay involving the conserved Tyr and Lys, as well as
Asn (or Ser). Some SDR family members, including 17
beta-hydroxysteroid dehydrogenase contain an additional
helix-turn-helix motif that is not generally found among
SDRs.
Length = 221
Score = 137 bits (346), Expect = 7e-42
Identities = 60/112 (53%), Positives = 82/112 (73%), Gaps = 2/112 (1%)
Query: 1 WVGSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTILAGDKIDAVICVAGGWAGGNA 60
WV SIDL N++ADA+IIV D++ EQ V+A + + K+DA+ICVAGGWAGG+A
Sbjct: 27 WVASIDLAENEEADASIIVLDSDSFTEQAKQVVASVARL--SGKVDALICVAGGWAGGSA 84
Query: 61 AAKDFVKSADIMWRQSVWSSVLAATIAANHLKPGGLVSLPGAKPALEGTPGM 112
+K FVK+ D+MW+Q++W+S +A+ +A HL GGL+ L GAK ALE TPGM
Sbjct: 85 KSKSFVKNWDLMWKQNLWTSFIASHLATKHLLSGGLLVLTGAKAALEPTPGM 136
>gnl|CDD|147776 pfam05804, KAP, Kinesin-associated protein (KAP). This family
consists of several eukaryotic kinesin-associated (KAP)
proteins. Kinesins are intracellular multimeric
transport motor proteins that move cellular cargo on
microtubule tracks. It has been shown that the sea
urchin KRP85/95 holoenzyme associates with a KAP115
non-motor protein, forming a heterotrimeric complex in
vitro, called the Kinesin-II.
Length = 708
Score = 31.0 bits (70), Expect = 0.14
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 8/42 (19%)
Query: 3 GSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTILAGDK 44
GSID++P+D+A +IVN E E T+L E+ + G++
Sbjct: 4 GSIDVHPSDKA---LIVN-----YELEATILGEMGDPMLGER 37
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.5 bits (67), Expect = 0.42
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 5 IDLNPNDQAD----ANIIVNKDDAWLEQETTVLAELKTILAGDKID 46
ID+ P D +D A II+N+ LE+ + LAE L +KID
Sbjct: 245 IDIAPIDGSDPVENARIIINE----LEKYSPKLAEKPRWLVFNKID 286
>gnl|CDD|216847 pfam02016, Peptidase_S66, LD-carboxypeptidase.
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a
peptide bond between a di-basic amino acid and the
C-terminal D-alanine in the tetrapeptide moiety in
peptidoglycan. This cleaves the bond between an L- and
a D-amino acid. The function of this activity is in
murein recycling. This family also includes the
microcin c7 self-immunity protein. This family
corresponds to Merops family S66.
Length = 281
Score = 29.0 bits (66), Expect = 0.44
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 33 LAELKTILAGDKIDAVICVAGGW 55
A+L A IDA+IC GG+
Sbjct: 50 AADLHAAFADPDIDAIICARGGY 72
>gnl|CDD|212497 cd11731, Lin1944_like_SDR_c, Lin1944 and related proteins,
classical (c) SDRs. Lin1944 protein from Listeria
Innocua is a classical SDR, it contains a glycine-rich
motif similar to the canonical motif of the SDR
NAD(P)-binding site. However, the typical SDR active
site residues are absent in this subgroup of proteins of
undetermined function. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 198
Score = 28.7 bits (65), Expect = 0.53
Identities = 11/58 (18%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 44 KIDAVICVAGGWAGGNAAAKDFVKSADIM--WRQSVWSSVLAATIAANHLKPGGLVSL 99
DA++ AG A AD + + +L GG ++L
Sbjct: 54 HFDAIVSTAGDAEFAPLAELT---DADFQRGLNSKLLGQINLVRHGLPYLNDGGSITL 108
>gnl|CDD|232900 TIGR00272, DPH2, diphthamide biosynthesis protein 2. This protein
has been shown in Saccharomyces cerevisiae to be one of
several required for the modification of a particular
histidine residue of translation elongation factor 2 to
diphthamide. This modified site can then become the
target for ADP-ribosylation by diphtheria toxin [Protein
fate, Protein modification and repair].
Length = 496
Score = 28.4 bits (63), Expect = 0.90
Identities = 7/36 (19%), Positives = 15/36 (41%)
Query: 8 NPNDQADANIIVNKDDAWLEQETTVLAELKTILAGD 43
+ I + D + + ++ + LK +L GD
Sbjct: 146 RAFPDLSSKICLMADAPFSKHQSQLYNILKEVLPGD 181
>gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease,
includes microcin C7 self immunity protein.
LD-carboxypeptidase (Muramoyltetrapeptide
carboxypeptidase; EC 3.4.17.13; Merops family S66;
initially described as Carboxypeptidase II) family also
includes the microcin c7 self-immunity protein (MccF)
as well as uncharacterized proteins including
hypothetical proteins. LD-carboxypeptidase hydrolyzes
the amide bond that links the dibasic amino acids to
C-terminal D-amino acids. The physiological substrates
of LD-carboxypeptidase are tetrapeptide fragments (such
as UDP-MurNAc-tetrapeptides) that are produced when
bacterial cell walls are degraded; they contain an
L-configured residue (L-lysine or meso-diaminopimelic
acid residue) as the penultimate residue and D-alanine
as the ultimate residue. A possible role of
LD-carboxypeptidase is in peptidoglycan recycling
whereby the resulting tripeptide (precursor for murein
synthesis) can be reconverted into peptidoglycan by
attachment of preformed D-Ala-D-Ala dipeptides. Some
enzymes possessing LD-carboxypeptidase activity also
act as LD-transpeptidase by replacing the terminal
D-Ala with another D-amino acid. MccF contributes to
self-immunity towards microcin C7 (MccC7), a
ribosomally encoded peptide antibiotic that contains a
phosphoramidate linkage to adenosine monophosphate at
its C-terminus. Its possible biological role is to
defend producer cells against exogenous microcin from
re-entering after having been exported. It is
suggested that MccF is involved in microcin degradation
or sequestration in the periplasm.
Length = 282
Score = 27.9 bits (63), Expect = 1.1
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 33 LAELKTILAGDKIDAVICVAGGW 55
A+L A +I A+ C GG+
Sbjct: 51 AADLNAAFADPEIKAIWCARGGY 73
>gnl|CDD|107202 cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily
(fold type II); this family of pyridoxal phosphate
(PLP)-dependent enzymes catalyzes beta-replacement and
beta-elimination reactions. This CD corresponds to
aminocyclopropane-1-carboxylate deaminase (ACCD),
tryptophan synthase beta chain (Trp-synth_B),
cystathionine beta-synthase (CBS), O-acetylserine
sulfhydrylase (CS), serine dehydratase (Ser-dehyd),
threonine dehydratase (Thr-dehyd), diaminopropionate
ammonia lyase (DAL), and threonine synthase (Thr-synth).
ACCD catalyzes the conversion of
1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate
and ammonia. Tryptophan synthase folds into a tetramer,
where the beta chain is the catalytic PLP-binding
subunit and catalyzes the formation of L-tryptophan from
indole and L-serine. CBS is a tetrameric hemeprotein
that catalyzes condensation of serine and homocysteine
to cystathionine. CS is a homodimer that catalyzes the
formation of L-cysteine from O-acetyl-L-serine.
Ser-dehyd catalyzes the conversion of L- or D-serine to
pyruvate and ammonia. Thr-dehyd is active as a homodimer
and catalyzes the conversion of L-threonine to
2-oxobutanoate and ammonia. DAL is also a homodimer and
catalyzes the alpha, beta-elimination reaction of both
L- and D-alpha, beta-diaminopropionate to form pyruvate
and ammonia. Thr-synth catalyzes the formation of
threonine and inorganic phosphate from
O-phosphohomoserine.
Length = 244
Score = 27.9 bits (63), Expect = 1.1
Identities = 16/38 (42%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 25 WLEQETTVLAELKTILAGDKIDAVICVAGGWAGGNAAA 62
Q T L E+ L G K DAV+ GG GGN A
Sbjct: 135 IAGQGTIGL-EILEQLGGQKPDAVVVPVGG--GGNIAG 169
>gnl|CDD|176915 cd08906, START_STARD3-like, Cholesterol-binding START domain of
mammalian STARD3 and related proteins. This subgroup
includes the steroidogenic acute regulatory protein
(StAR)-related lipid transfer (START) domains of STARD3
(also known as metastatic lymph node 64/MLN64) and
related proteins. It belongs to the START domain family,
and in turn to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. STARD3 has a high affinity for cholesterol. It
may function in trafficking endosomal cholesterol to a
cytosolic acceptor or membrane. In addition to having a
cytoplasmic START cholesterol-binding domain, STARD3
also contains an N-terminal MENTAL cholesterol-binding
and protein-protein interaction domain. The MENTAL
domain contains transmembrane helices and anchors MLN64
to endosome membranes. The gene encoding STARD3 is
overexpressed in about 25% of breast cancers.
Length = 209
Score = 27.5 bits (61), Expect = 1.5
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 16/66 (24%)
Query: 51 VAGGWAGGNAAAKDFVKSADIMWRQSVWSSVLAATIAANHLK-------------PGGLV 97
VA G AGG + +DFV I R+ + ++A I+ H PGG V
Sbjct: 101 VAAGAAGGVVSPRDFVNVRRIERRRDRY---VSAGISTTHSHKPPLSKYVRGENGPGGFV 157
Query: 98 SLPGAK 103
L A
Sbjct: 158 VLKSAS 163
>gnl|CDD|239567 cd03485, MutL_Trans_hPMS_1_like, MutL_Trans_hPMS1_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM1 (hPSM1) and yeast
MLH2. hPSM1 and yMLH2 are members of the DNA mismatch
repair (MutL/MLH1/PMS2) family. This transducer domain
is homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. PMS1 forms a heterodimer with
MLH1. The MLH1-PMS1 complex functions in meiosis. Loss
of yMLH2 results in a small but significant decrease in
spore viability and a significant increase in gene
conversion frequencies. A role for hMLH1-hPMS1 in DNA
mismatch repair has not been established. Mutation in
hMLH1 accounts for a large fraction of Lynch syndrome
(HNPCC) families, however there is no convincing
evidence to support hPMS1 having a role in HNPCC
predisposition.
Length = 132
Score = 26.5 bits (59), Expect = 2.8
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 1 WVGSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTIL 40
+ +I P D NI +KDD L+ + VL ++ +L
Sbjct: 89 FFLNILCPPGL-VDVNIEPDKDDVLLQNKEAVLQAVENLL 127
>gnl|CDD|132883 cd07062, Peptidase_S66_mccF_like, Microcin C7 self-immunity
protein determines resistance to exogenous microcin C7.
Microcin C7 self-immunity protein (mccF): MccF, a
homolog of the LD-carboxypeptidase family, mediates
resistance against exogenously added microcin C7
(MccC7), a ribosomally-encoded peptide antibiotic that
contains a phosphoramidate linkage to adenosine
monophosphate at its C-terminus. The plasmid-encoded
mccF gene is transcribed in the opposite direction to
the other five genes (mccA-E) and is required for the
full expression of immunity but not for production. The
catalytic triad residues (Ser, His, Glu) of
LD-carboxypeptidase are also conserved in MccF,
strongly suggesting that MccF shares the hydrolytic
activity with LD-carboxypeptidases. Substrates of MccF
have not been deduced, but could likely be microcin C7
precursors. The possible role of MccF is to defend
producer cells against exogenous microcin from
re-entering after having been exported. It is
suggested that MccF is involved in microcin degradation
or sequestration in the periplasm.
Length = 308
Score = 26.8 bits (60), Expect = 3.5
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 33 LAELKTILAGDKIDAVICVAGG 54
EL A I A+I GG
Sbjct: 55 AEELMAAFADPSIKAIIPTIGG 76
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 26.4 bits (59), Expect = 3.5
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 13/94 (13%)
Query: 2 VGSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTILAGDKIDAVICVAGGWAGGNAA 61
+ ++D+ P +I + D E L +L L G +D V+ A
Sbjct: 73 IVAVDILPMKP-IPGVIFLQGDITDE---DTLEKLLEALGGAPVDVVLSDM-------AP 121
Query: 62 AKDFVKSADIMWRQSVWSSVLAATIAANHLKPGG 95
+S D +S++ LA A LKPGG
Sbjct: 122 NTSGNRSVDHA--RSMYLCELALEFALEVLKPGG 153
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 25.5 bits (57), Expect = 9.5
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 8/35 (22%)
Query: 22 DDAWLEQETTV---LAELK-----TILAGDKIDAV 48
D EQ V L EL +L +KID +
Sbjct: 280 DPDREEQIEAVEKVLEELGAEDIPQLLVYNKIDLL 314
>gnl|CDD|233056 TIGR00619, sbcd, exonuclease SbcD. All proteins in this family
for which functions are known are double-stranded DNA
exonuclease (as part of a complex with SbcC homologs).
This complex functions in the initiation of
recombination and recombinational repair and is
particularly important in regulating the stability of
DNA sections that can form secondary structures. This
family is likely homologous to the MRE11 family. This
family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 253
Score = 25.5 bits (56), Expect = 9.8
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 26 LEQETTVLAELKTILAGDKIDAVICVAG 53
L ++ L +L ++IDA++ VAG
Sbjct: 21 LAEQKAFLDDLLEFAKAEQIDALL-VAG 47
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 0.133 0.415
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,361,713
Number of extensions: 550058
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 612
Number of HSP's successfully gapped: 37
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (21.7 bits)
S2: 53 (24.1 bits)