RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5125
(227 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 = 129 bits (327), Expect = 2e-37
Identities = 58/110 (52%), Positives = 80/110 (72%), Gaps = 2/110 (1%)
Query: 118 WVGSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTILAGDKIDAVICVAGGWAGGNA 177
WV SIDL N++ADA+IIV D++ EQ V+A + + K+DA+ICVAGGWAGG+A
Sbjct: 27 WVASIDLAENEEADASIIVLDSDSFTEQAKQVVASVARL--SGKVDALICVAGGWAGGSA 84
Query: 178 AAKDFVKSADIMWRQSVWSSVLAATIAANHLKPGGLVSLPGAKPALEGTP 227
+K FVK+ D+MW+Q++W+S +A+ +A HL GGL+ L GAK ALE TP
Sbjct: 85 KSKSFVKNWDLMWKQNLWTSFIASHLATKHLLSGGLLVLTGAKAALEPTP 134
Score = 98.6 bits (246), Expect = 2e-25
Identities = 43/83 (51%), Positives = 60/83 (72%), Gaps = 2/83 (2%)
Query: 23 QETTVLAELKTILAGDKIDAVICVAGGWAGGNAAAKDFVKSADIMWRQSVWSSVLAATIA 82
Q V+A + + K+DA+ICVAGGWAGG+A +K FVK+ D+MW+Q++W+S +A+ +A
Sbjct: 54 QAKQVVASVARL--SGKVDALICVAGGWAGGSAKSKSFVKNWDLMWKQNLWTSFIASHLA 111
Query: 83 ANHLKPGGLVSLPGAKPALEGTP 105
HL GGL+ L GAK ALE TP
Sbjct: 112 TKHLLSGGLLVLTGAKAALEPTP 134
>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 = 30.6 bits (69), Expect = 0.80
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 8/42 (19%)
Query: 120 GSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTILAGDK 161
GSID++P+D+A +IVN E E T+L E+ + G++
Sbjct: 4 GSIDVHPSDKA---LIVN-----YELEATILGEMGDPMLGER 37
>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 = 29.4 bits (67), Expect = 1.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 28 LAELKTILAGDKIDAVICVAGGW 50
A+L A IDA+IC GG+
Sbjct: 50 AADLHAAFADPDIDAIICARGGY 72
Score = 29.4 bits (67), Expect = 1.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 150 LAELKTILAGDKIDAVICVAGGW 172
A+L A IDA+IC GG+
Sbjct: 50 AADLHAAFADPDIDAIICARGGY 72
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 29.5 bits (67), Expect = 1.4
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 122 IDLNPNDQAD----ANIIVNKDDAWLEQETTVLAELKTILAGDKID 163
ID+ P D +D A II+N+ LE+ + LAE L +KID
Sbjct: 245 IDIAPIDGSDPVENARIIINE----LEKYSPKLAEKPRWLVFNKID 286
>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 = 2.0
Identities = 11/58 (18%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 39 KIDAVICVAGGWAGGNAAAKDFVKSADIM--WRQSVWSSVLAATIAANHLKPGGLVSL 94
DA++ AG A AD + + +L GG ++L
Sbjct: 54 HFDAIVSTAGDAEFAPLAELT---DADFQRGLNSKLLGQINLVRHGLPYLNDGGSITL 108
Score = 28.7 bits (65), Expect = 2.0
Identities = 11/58 (18%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 161 KIDAVICVAGGWAGGNAAAKDFVKSADIM--WRQSVWSSVLAATIAANHLKPGGLVSL 216
DA++ AG A AD + + +L GG ++L
Sbjct: 54 HFDAIVSTAGDAEFAPLAELT---DADFQRGLNSKLLGQINLVRHGLPYLNDGGSITL 108
>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 = 28.3 bits (64), Expect = 3.0
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 28 LAELKTILAGDKIDAVICVAGGW 50
A+L A +I A+ C GG+
Sbjct: 51 AADLNAAFADPEIKAIWCARGGY 73
Score = 28.3 bits (64), Expect = 3.0
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 150 LAELKTILAGDKIDAVICVAGGW 172
A+L A +I A+ C GG+
Sbjct: 51 AADLNAAFADPEIKAIWCARGGY 73
>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 = 3.4
Identities = 7/36 (19%), Positives = 15/36 (41%)
Query: 125 NPNDQADANIIVNKDDAWLEQETTVLAELKTILAGD 160
+ I + D + + ++ + LK +L GD
Sbjct: 146 RAFPDLSSKICLMADAPFSKHQSQLYNILKEVLPGD 181
>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 = 4.4
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 16/66 (24%)
Query: 46 VAGGWAGGNAAAKDFVKSADIMWRQSVWSSVLAATIAANHLK-------------PGGLV 92
VA G AGG + +DFV I R+ + ++A I+ H PGG V
Sbjct: 101 VAAGAAGGVVSPRDFVNVRRIERRRDRY---VSAGISTTHSHKPPLSKYVRGENGPGGFV 157
Query: 93 SLPGAK 98
L A
Sbjct: 158 VLKSAS 163
Score = 27.5 bits (61), Expect = 4.4
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 16/66 (24%)
Query: 168 VAGGWAGGNAAAKDFVKSADIMWRQSVWSSVLAATIAANHLK-------------PGGLV 214
VA G AGG + +DFV I R+ + ++A I+ H PGG V
Sbjct: 101 VAAGAAGGVVSPRDFVNVRRIERRRDRY---VSAGISTTHSHKPPLSKYVRGENGPGGFV 157
Query: 215 SLPGAK 220
L A
Sbjct: 158 VLKSAS 163
>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 = 27.5 bits (62), Expect = 5.1
Identities = 16/38 (42%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 142 WLEQETTVLAELKTILAGDKIDAVICVAGGWAGGNAAA 179
Q T L E+ L G K DAV+ GG GGN A
Sbjct: 135 IAGQGTIGL-EILEQLGGQKPDAVVVPVGG--GGNIAG 169
>gnl|CDD|233594 TIGR01844, type_I_sec_TolC, type I secretion outer membrane
protein, TolC family. Members of This model are outer
membrane proteins from the TolC subfamily within the RND
(Resistance-Nodulation-cell Division) efflux systems.
These proteins, unlike the NodT subfamily, appear not to
be lipoproteins. All are believed to participate in type
I protein secretion, an ABC transporter system for
protein secretion without cleavage of a signal sequence,
although they may, like TolC, participate also in the
efflux of smaller molecules as well. This family
includes the well-documented examples TolC (E. coli),
PrtF (Erwinia), and AprF (Pseudomonas aeruginosa)
[Protein fate, Protein and peptide secretion and
trafficking, Transport and binding proteins, Porins].
Length = 415
Score = 27.7 bits (62), Expect = 5.2
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 93 SLPGAKPALEGTPANVDVAMELLYNWVGSIDLNP 126
A+ L N+D A L VG +L P
Sbjct: 166 RYASARAQLIQAQNNLDDAKAQLRRLVGQPELAP 199
>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 = 27.1 bits (61), Expect = 8.0
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 28 LAELKTILAGDKIDAVICVAGG 49
EL A I A+I GG
Sbjct: 55 AEELMAAFADPSIKAIIPTIGG 76
Score = 27.1 bits (61), Expect = 8.0
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 150 LAELKTILAGDKIDAVICVAGG 171
EL A I A+I GG
Sbjct: 55 AEELMAAFADPSIKAIIPTIGG 76
>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 = 8.0
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 118 WVGSIDLNPNDQADANIIVNKDDAWLEQETTVLAELKTIL 157
+ +I P D NI +KDD L+ + VL ++ +L
Sbjct: 89 FFLNILCPPGL-VDVNIEPDKDDVLLQNKEAVLQAVENLL 127
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
0.316 0.131 0.394
Gapped
Lambda K H
0.267 0.0628 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,471,799
Number of extensions: 1077748
Number of successful extensions: 1179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1176
Number of HSP's successfully gapped: 36
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
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: 57 (25.9 bits)