RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15639
(135 letters)
>gnl|CDD|222758 pfam14446, Prok-RING_1, Prokaryotic RING finger family 1. RING
finger family found sporadically in bacteria and
archaea, and associated in gene neighborhoods with
other components of the ubiquitin-based signaling and
degradation system, including ubiquitin, the E1 and E2
proteins and the JAB-like metallopeptidase. The
bacterial versions contain transmembrane helices.
Length = 55
Score = 32.0 bits (73), Expect = 0.010
Identities = 13/31 (41%), Positives = 14/31 (45%)
Query: 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASY 43
C VC K FKP D VC EC +C
Sbjct: 8 CPVCGKKFKPGDDIVVCPECGAPYHRECWEK 38
>gnl|CDD|237600 PRK14072, PRK14072, 6-phosphofructokinase; Provisional.
Length = 416
Score = 30.2 bits (69), Expect = 0.29
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 6 PAARLGNCRVCLKSFKPD--DYSRVC 29
P+ LG+CR LKS + D +Y R+
Sbjct: 71 PSGALGSCRYKLKSLEEDRAEYERLL 96
>gnl|CDD|180659 PRK06690, PRK06690, acetyl-CoA acetyltransferase; Provisional.
Length = 361
Score = 29.7 bits (67), Expect = 0.39
Identities = 17/67 (25%), Positives = 22/67 (32%), Gaps = 15/67 (22%)
Query: 63 KLQSRAQPVLSQNST----------DSLLDVPVLEALQRRHSDVK-----IGSANSGAHP 107
++ R +P N T D V V+E Q R K + SA G P
Sbjct: 194 RIIKRTKPAFLHNGTVTAGNSCGVNDGACAVLVMEEGQARKLGYKPVLRFVRSAVVGVDP 253
Query: 108 ANQGLAP 114
G P
Sbjct: 254 NLPGTGP 260
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 27.7 bits (62), Expect = 0.39
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 13 CRVCLKSFKPDDYSRVCYEC-HQKVCEDCASYSKLDENQDENTWRCSICRRKLQSR 67
C +CL+ + + V C H +CE+CA + +C ICR+ ++S
Sbjct: 5 CVICLERPR----NVVFLPCGHLCLCEECAKRLRS-------KKKCPICRQPIESV 49
>gnl|CDD|215603 PLN03145, PLN03145, Protein phosphatase 2c; Provisional.
Length = 365
Score = 29.5 bits (66), Expect = 0.55
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 90 QRRHSDVKIGSANSGAHPANQGLAPPRSPELRRHSDV--SPASLKELE 135
+ S G ++ G P N +A P L RHS + +PAS +E
Sbjct: 2 TKGISGGGEGGSSGGGRPPNPSVAACCKPSLVRHSSLVKTPASDISVE 49
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 29.1 bits (65), Expect = 0.75
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 13 CRVCLKSFKPDDYSRV---CYECHQKVCEDCASYSKLDENQ 50
CRVC + + C+ C VC+ C Y + + NQ
Sbjct: 18 CRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQ 58
>gnl|CDD|239139 cd02674, Peptidase_C19R, A subfamily of peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 230
Score = 27.3 bits (61), Expect = 2.3
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 15/67 (22%)
Query: 13 CRVCLKS---FKPDDY--------SRVCYECHQKVCEDC-ASYSKLDENQDENTWRCSIC 60
C C K+ F+P Y S + EDC ++K + +N W+C C
Sbjct: 54 CLTCGKTSTTFEPFTYLSLPIPSGSGDAPKV---TLEDCLRLFTKEETLDGDNAWKCPKC 110
Query: 61 RRKLQSR 67
++K ++
Sbjct: 111 KKKRKAT 117
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one
of the best studied FHL proteins. FHL2 expression is
most abundant in the heart, and in brain, liver and
lung at lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 62
Score = 25.6 bits (56), Expect = 2.9
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 25 YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64
YS C EC + + DC S D + E+ + C C+ L
Sbjct: 1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSL 40
>gnl|CDD|215138 PLN02248, PLN02248, cellulose synthase-like protein.
Length = 1135
Score = 27.3 bits (61), Expect = 2.9
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 8/80 (10%)
Query: 31 ECHQKVCEDCASYSKLDENQDENTWRCSICRRKLQSRAQPVLSQNSTDSLLDVPVLEA-- 88
EC K+C DC + ++ C C+ + + + L +P
Sbjct: 149 ECGFKICRDC------YIDAVKSGGICPGCKEPYKVTDLDDEVPDESSGALPLPPPGGSK 202
Query: 89 LQRRHSDVKIGSANSGAHPA 108
+ RR S +K S +
Sbjct: 203 MDRRLSLMKSNSLLMRSQTG 222
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain
with a consensus sequence equivalent to the C-terminal
half of a LIM domain. LIMPETin is an exception,
containing six LIM domains. FHL1, 2 and 3 are
predominantly expressed in muscle tissues, and FHL5 is
highly expressed in male germ cells. FHL proteins
exert their roles as transcription co-activators or
co-repressors through a wide array of interaction
partners. For example, FHL1 binds to Myosin-binding
protein C, regulating myosin filament formation and
sarcomere assembly. FHL2 has shown to interact with
more than 50 different proteins, including receptors,
structural proteins, transcription factors and
cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
FHL3 int eracts with many transcription factors, such
as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 25.5 bits (56), Expect = 3.5
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 25 YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64
++ C EC +K+ D S D + E ++C C+R L
Sbjct: 1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSL 40
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 25.3 bits (55), Expect = 4.0
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 25 YSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64
++ C EC + + D D + E+ +RC C R L
Sbjct: 1 FANTCDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSL 40
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 24.7 bits (54), Expect = 4.5
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 7/53 (13%)
Query: 11 GNCRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRK 63
C +CL F+P + V C ++C ++ C +CR
Sbjct: 1 DECPICLDEFEPGEEVVVL-PCGHVFHKECLDKWL------RSSNTCPLCRAP 46
>gnl|CDD|143402 cd07083, ALDH_P5CDH, ALDH subfamily NAD+-dependent
delta(1)-pyrroline-5-carboxylate dehydrogenase-like.
ALDH subfamily of the NAD+-dependent,
delta(1)-pyrroline-5-carboxylate dehydrogenases (P5CDH,
EC=1.5.1.12). The proline catabolic enzymes, proline
dehydrogenase and P5CDH catalyze the two-step oxidation
of proline to glutamate. P5CDH catalyzes the oxidation
of glutamate semialdehyde, utilizing NAD+ as the
electron acceptor. In some bacteria, the two enzymes are
fused into the bifunctional flavoenzyme, proline
utilization A (PutA). These enzymes play important roles
in cellular redox control, superoxide generation, and
apoptosis. In certain prokaryotes such as Escherichia
coli, PutA is also a transcriptional repressor of the
proline utilization genes. Monofunctional enzyme
sequences such as those seen in the Bacillus RocA P5CDH
are also present in this subfamily as well as the human
ALDH4A1 P5CDH and the Drosophila Aldh17 P5CDH.
Length = 500
Score = 26.4 bits (58), Expect = 5.1
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 12/48 (25%)
Query: 56 RCSICRRKLQSRAQPVLSQNSTDSLLDVPVLEALQRRHSDVKIGSANS 103
+CS R +L+Q + + PVLE L +R + +G
Sbjct: 302 KCSAASRL-------ILTQGAYE-----PVLERLLKRAERLSVGPPEE 337
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 24.4 bits (53), Expect = 5.2
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 29 CYECHQKVCEDCASYS 44
C +C Q +CE+CA
Sbjct: 18 CEDCQQLLCEECALSG 33
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 24.3 bits (53), Expect = 5.6
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 8/52 (15%)
Query: 13 CRVCLKSFKPDDYSRVCYECHQKVCEDCASYSKLDENQDENTWRCSICRRKL 64
C +CL+ F+ V C C C +D+ C +CR +
Sbjct: 2 CPICLEEFREP---VVLLPCGHVFCRSC-----IDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|173705 cd05614, STKc_MSK2_N, N-terminal catalytic domain of the Protein
Serine/Threonine Kinase, Mitogen and stress-activated
kinase 2. Serine/Threonine Kinases (STKs), Mitogen and
stress-activated kinase (MSK) subfamily, MSK2,
N-terminal catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The MSK
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. MSKs contain an N-terminal kinase domain (NTD)
from the AGC family and a C-terminal kinase domain (CTD)
from the CAMK family, similar to 90 kDa ribosomal
protein S6 kinases (RSKs). MSKs are activated by two
major signaling cascades, the Ras-MAPK and p38 stress
kinase pathways, which trigger phosphorylation in the
activation loop (A-loop) of the CTD of MSK. The active
CTD phosphorylates the hydrophobic motif (HM) of NTD,
which facilitates the phosphorylation of the A-loop and
activates the NTD, which in turn phosphorylates
downstream targets. MSK2 and MSK1 play nonredundant
roles in activating histone H3 kinases, which play
pivotal roles in compaction of the chromatin fiber. MSK2
is the required H3 kinase in response to stress stimuli
and activation of the p38 MAPK pathway. MSK2 also plays
a role in the pathogenesis of psoriasis.
Length = 332
Score = 25.7 bits (56), Expect = 8.3
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 15/58 (25%)
Query: 85 VLEALQRRHSDVKIGSANSGA-----HPANQGL----------APPRSPELRRHSDVS 127
+L L R+ ++G+ GA HP +GL PP P +R DV
Sbjct: 241 LLHKLLRKDPKKRLGAGPQGASEIKEHPFFKGLDWEALALRKVNPPFRPSIRNELDVG 298
>gnl|CDD|99964 cd03789, GT1_LPS_heptosyltransferase, Lipopolysaccharide
heptosyltransferase is involved in the biosynthesis of
lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is
a major component of the outer membrane of
gram-negative bacteria. LPS heptosyltransferase
transfers heptose molecules from ADP-heptose to
3-deoxy-D-manno-octulosonic acid (KDO), a part of the
inner core component of LPS. This family belongs to the
GT-B structural superfamily of glycoslytransferases,
which have characteristic N- and C-terminal domains
each containing a typical Rossmann fold. The two
domains have high structural homology despite minimal
sequence homology. The large cleft that separates the
two domains includes the catalytic center and permits a
high degree of flexibility.
Length = 279
Score = 25.7 bits (57), Expect = 8.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 78 DSLLDVPVLEALQRRHSDVKI 98
D +L P+L AL+ R+ D +I
Sbjct: 12 DVVLATPLLRALKARYPDARI 32
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 0.129 0.395
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,440,818
Number of extensions: 519596
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 54
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (24.2 bits)