RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8930
(65 letters)
>gnl|CDD|187608 cd05350, SDR_c6, classical (c) SDR, subgroup 6. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a fairly well conserved typical
Gly-rich NAD-binding motif. 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 = 239
Score = 29.6 bits (67), Expect = 0.068
Identities = 11/43 (25%), Positives = 22/43 (51%)
Query: 3 SLLGLLSPKDAASHIIRAQRRGESQVAVPNGLLHVNNFCRLMP 45
++ L+S + AA I +A ++G ++ P L +L+P
Sbjct: 190 TMPFLMSVEQAAKRIYKAIKKGAAEPTFPWRLAVPLRLLKLLP 232
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 26.8 bits (60), Expect = 0.57
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 8 LSPKDAASHIIRAQRRGESQVAVPNGLLHVNNFCRLMPLKVARILKDFLDSG 59
+ P+D A+ I+ + +V VP L + RL+P +V L L
Sbjct: 200 VEPEDVAAAIVGTVAKPRPEVRVPRALGPLAQAQRLLPRRVREALNRLLGGD 251
>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I
lysyl tRNA synthetase. Class I lysyl tRNA synthetase
(LysRS) catalytic core domain. This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in
ATP binding. The class I LysRS is found only in archaea
and some bacteria and has evolved separately from class
II LysRS, as the two do not share structural or
sequence similarity.
Length = 353
Score = 26.1 bits (58), Expect = 1.3
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 31 PNGLLHVNNFCRLMPLKVARILKDFLDSGVDSDLL 65
P+G +H+ NF ++ + + D G + L+
Sbjct: 29 PSGHIHIGNFREVI--TADLVARALRDLGFEVRLI 61
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. 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 = 243
Score = 24.9 bits (55), Expect = 3.6
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 1 FPSLLGLLSPKDAASHIIRAQRRGESQVAVP 31
P L +L P+ A I+RA + + +P
Sbjct: 196 RPLLAPILEPEYVAEKIVRAILTNQQMLYLP 226
>gnl|CDD|237914 PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
Length = 903
Score = 24.2 bits (53), Expect = 5.3
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 40 FCRLMPLKVARILK 53
F +L PL+ +R+LK
Sbjct: 618 FAKLTPLQKSRVLK 631
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five
recognizable domains. Amino-acid sequence homology of
SMC proteins between species is largely confined to the
amino- and carboxy-terminal globular domains. The
amino-terminal domain contains a 'Walker A'
nucleotide-binding domain (GxxGxGKS/T, in the
single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B'
motif, and a motif with homology to the signature
sequence of the ATP-binding cassette (ABC) family of
ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 23.3 bits (51), Expect = 9.8
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 2 PSLLGLLSPKDAASHIIRAQRRG--ESQVAVPNGLLHVNNFCRLMP 45
P LLG K + R G E ++ G + V+N C+ +P
Sbjct: 51 PKLLG--RAKKVGEFVKRGCDEGTIEIELYGNPGNIQVDNLCQFLP 94
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
0.324 0.141 0.410
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,287,069
Number of extensions: 237404
Number of successful extensions: 326
Number of sequences better than 10.0: 1
Number of HSP's gapped: 326
Number of HSP's successfully gapped: 8
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.2 bits)