RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17303
(159 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 = 97.0 bits (242), Expect = 1e-25
Identities = 43/97 (44%), Positives = 64/97 (65%), Gaps = 2/97 (2%)
Query: 63 SADNTLIPLLFWTQIETTVLAELKTILAGDKIDAVICVAGGWAVGNAAAKDFVKSADIMW 122
A ++ +T+ V+A + + K+DA+ICVAGGWA G+A +K FVK+ D+MW
Sbjct: 40 DASIIVLDSDSFTEQAKQVVASVARL--SGKVDALICVAGGWAGGSAKSKSFVKNWDLMW 97
Query: 123 RQSVWSSVLAATIAANHLKPGGLVSLPGAKPALEGTP 159
+Q++W+S +A+ +A HL GGL+ L GAK ALE TP
Sbjct: 98 KQNLWTSFIASHLATKHLLSGGLLVLTGAKAALEPTP 134
>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 = 32.1 bits (74), Expect = 0.097
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 13/50 (26%)
Query: 28 LAELKTILAGDKIDAVICVAGGWAGGNAAAKDFVKSADNTLIPLLFWTQI 77
A+L A IDA+IC GG+ A N L+P L + I
Sbjct: 50 AADLHAAFADPDIDAIICARGGY---GA----------NRLLPYLDYDLI 86
Score = 29.4 bits (67), Expect = 0.71
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 82 LAELKTILAGDKIDAVICVAGGW 104
A+L A IDA+IC GG+
Sbjct: 50 AADLHAAFADPDIDAIICARGGY 72
>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 = 29.5 bits (67), Expect = 0.62
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 13/51 (25%)
Query: 28 LAELKTILAGDKIDAVICVAGGWAGGNAAAKDFVKSADNTLIPLLFWTQIE 78
A+L A +I A+ C GG+ A N L+P L + I
Sbjct: 51 AADLNAAFADPEIKAIWCARGGY---GA----------NRLLPYLDYDLIR 88
Score = 28.3 bits (64), Expect = 1.8
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 82 LAELKTILAGDKIDAVICVAGGW 104
A+L A +I A+ C GG+
Sbjct: 51 AADLNAAFADPEIKAIWCARGGY 73
>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 = 29.1 bits (66), Expect = 0.72
Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 5/58 (8%)
Query: 93 KIDAVICVAGGWAVGNAAAKDFVKSADIM--WRQSVWSSVLAATIAANHLKPGGLVSL 148
DA++ AG A + AD + + +L GG ++L
Sbjct: 54 HFDAIVSTAG---DAEFAPLAELTDADFQRGLNSKLLGQINLVRHGLPYLNDGGSITL 108
>gnl|CDD|223577 COG0503, Apt, Adenine/guanine phosphoribosyltransferases and
related PRPP-binding proteins [Nucleotide transport and
metabolism].
Length = 179
Score = 28.4 bits (64), Expect = 1.2
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 57 AKDFVKSADNTLI--PLLFWTQIETTVLAELKTILAGDKIDAVICV-AGGWAVGNAAA 111
DF K + LL ++ ++ EL D ID ++ + A G + A A
Sbjct: 15 IPDFPKGGILFVDITLLLGDPELLAKLIDELAERYKDDGIDKIVTIEARGIPLAAAVA 72
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 28.6 bits (64), Expect = 1.4
Identities = 14/30 (46%), Positives = 15/30 (50%)
Query: 83 AELKTILAGDKIDAVICVAGGWAVGNAAAK 112
A L IL ID VI AG AVG + K
Sbjct: 63 ALLTEILHDHAIDTVIHFAGLKAVGESVQK 92
>gnl|CDD|180626 PRK06565, PRK06565, amidase; Validated.
Length = 566
Score = 28.2 bits (63), Expect = 1.9
Identities = 30/94 (31%), Positives = 38/94 (40%), Gaps = 20/94 (21%)
Query: 59 DFVKSADNTLIPLLFWTQI----------ETTVLAELKTILAGDKIDAVI--CVAGGWAV 106
++V A L W QI E T +L+ + G +DAV+ VA V
Sbjct: 425 EYVNMAKRGLKS---WDQIPTLPDGLRGLEKTRKLDLEDWMDGLGLDAVLFPTVAD---V 478
Query: 107 GNAAAKDFVKSADIMWRQSVWSSVLAATIAANHL 140
G A A SADI W VW V +A HL
Sbjct: 479 GPADADVNPASADIAWSNGVW--VANGNLAIRHL 510
>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 = 5.2
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 28 LAELKTILAGDKIDAVICVAGG 49
EL A I A+I GG
Sbjct: 55 AEELMAAFADPSIKAIIPTIGG 76
Score = 26.8 bits (60), Expect = 5.2
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 82 LAELKTILAGDKIDAVICVAGG 103
EL A I A+I GG
Sbjct: 55 AEELMAAFADPSIKAIIPTIGG 76
>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
Length = 352
Score = 26.8 bits (60), Expect = 5.6
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 83 AELKTILAGDKIDAVICVAGGWAVGNAAAK 112
L+ + A + DAVI AG AVG + AK
Sbjct: 71 EALEKVFASTRFDAVIHFAGLKAVGESVAK 100
>gnl|CDD|182645 PRK10682, PRK10682, putrescine transporter subunit:
periplasmic-binding component of ABC superfamily;
Provisional.
Length = 370
Score = 26.7 bits (59), Expect = 6.1
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 44 ICVAGGWAGGNAAAKDFVKSADN 66
ICVA GWAG A + K A N
Sbjct: 238 ICVAIGWAGDVWQASNRAKEAKN 260
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
0.321 0.135 0.415
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,973,873
Number of extensions: 717369
Number of successful extensions: 915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 914
Number of HSP's successfully gapped: 32
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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: 55 (25.0 bits)