RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2324
(170 letters)
>gnl|CDD|205516 pfam13336, AcetylCoA_hyd_C, Acetyl-CoA hydrolase/transferase
C-terminal domain. This family contains several enzymes
which take part in pathways involving acetyl-CoA.
Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation
of acetate from acetyl-CoA, CoA transferase (CAT1)
EC:2.8.3.- produces succinyl-CoA, and acetate-CoA
transferase EC:2.8.3.8 utilises acyl-CoA and acetate to
form acetyl-CoA.
Length = 152
Score = 134 bits (339), Expect = 7e-41
Identities = 41/81 (50%), Positives = 56/81 (69%)
Query: 55 GDKPLYDFVHNNELVQMKRGTYSNDPAIIRQNHRMTAINTCLEIDITGQVVSDSLGTRIY 114
G + LYDF+ +N ++M+ Y NDP +I QN M +IN+ LE+D+TGQV S+S+G R Y
Sbjct: 1 GSQRLYDFLDDNPKIEMRPVDYVNDPEVIAQNDNMVSINSALEVDLTGQVNSESIGGRQY 60
Query: 115 SGFGGQVDFMRGALTGLDGKG 135
SG GGQ+DF+RGA GK
Sbjct: 61 SGVGGQLDFVRGAYLSKGGKS 81
>gnl|CDD|223504 COG0427, ACH1, Acetyl-CoA hydrolase [Energy production and
conversion].
Length = 501
Score = 113 bits (285), Expect = 5e-30
Identities = 46/129 (35%), Positives = 75/129 (58%), Gaps = 8/129 (6%)
Query: 2 IPEAILSNIKHQI--NLGVHTELLTPGVIKLFNSGVINNSKKSIDRGQITATLLLGDKPL 59
IP A++ +K +LGVHTE+L G++ L G + N+ K+ + +G + L
Sbjct: 269 IPNAVMGGLKESPFKDLGVHTEVLQDGLVDLIEEGKVTNASKT----SFVLSFAMGSRKL 324
Query: 60 YDFVHNNELVQMKRGTYSNDPAIIRQNHRMTAINTCLEIDITGQVVSDSL-GTRIYSGFG 118
YD+++ N + ++ YSN+P IIR+ + AIN+ LE+D+ G V S + G+R +G G
Sbjct: 325 YDYLNYNPRIVLRPQDYSNNPEIIRRLG-VIAINSALEVDLYGAVNSTHVGGSRQMNGIG 383
Query: 119 GQVDFMRGA 127
G DF+R A
Sbjct: 384 GSGDFVRNA 392
>gnl|CDD|188463 TIGR03948, butyr_acet_CoA, butyryl-CoA:acetate CoA-transferase.
This enzyme represents one of at least two mechanisms
for reclaiming CoA from butyryl-CoA at the end of
butyrate biosynthesis (an important process performed by
some colonic bacteria), namely transfer of CoA to
acetate. An alternate mechanism transfers the butyrate
onto inorganic phosphate, after which butyrate kinase
transfers the phosphate onto ADP, creating ATP [Energy
metabolism, Fermentation].
Length = 445
Score = 94.1 bits (234), Expect = 4e-23
Identities = 45/120 (37%), Positives = 66/120 (55%)
Query: 15 NLGVHTELLTPGVIKLFNSGVINNSKKSIDRGQITATLLLGDKPLYDFVHNNELVQMKRG 74
+LGVHTE+ + + +G IN SKK+IDRG+ G K +YD++ +N
Sbjct: 238 DLGVHTEMYVDAFVDIAKAGKINGSKKNIDRGRQVYAFGAGTKKMYDYLDDNPECMSAPV 297
Query: 75 TYSNDPAIIRQNHRMTAINTCLEIDITGQVVSDSLGTRIYSGFGGQVDFMRGALTGLDGK 134
Y+ND I +IN ++ID+ GQV ++S G + SG GGQ+DF+ GA GK
Sbjct: 298 DYTNDIRSISALDNFISINNAVDIDLFGQVNAESAGIKQISGAGGQLDFVLGAYLSKGGK 357
>gnl|CDD|234217 TIGR03458, YgfH_subfam, succinate CoA transferase. This family of
CoA transferases includes enzymes catalyzing at least
two related but distinct activities. The E. coli YgfH
protein has been characterized as a
propionyl-CoA:succinate CoA transferase where it appears
to be involved in a pathway for the decarboxylation of
succinate to propionate. The Clostridium kluyveri CAT1
protein has been characterized as a acetyl-CoA:succinate
CoA transferase and is believed to be involved in
anaerobic succinate degradation. The
propionate:succinate transferase activity has been
reported in the propionic acid fermentation of
propionibacterium species where it is distinct from the
coupled activities of distinct nucleotide-triphosphate
dependent succinate and propionate/acetate CoA
transferases (as inferred from activity in the absence
of NTPs). The family represented by this model includes
a member from Propionibacterium acnes KPA171202 which is
likely to be responsible for this activity. A closely
related clade not included in this family are the Ach1p
proteins of fungi which are acetyl-CoA hydrolases. This
name has been applied to many of the proteins modeled by
This model, possibly erroneously.
Length = 485
Score = 45.3 bits (108), Expect = 5e-06
Identities = 26/55 (47%), Positives = 32/55 (58%), Gaps = 6/55 (10%)
Query: 76 YSNDPAIIRQNHRM--TAINTCLEIDITGQVVSDS-LGTRIYSGFGGQVDFMRGA 127
SN P IIR R+ AINT +E DI G V S +GT++ +G GG DF R A
Sbjct: 331 ISNHPEIIR---RLGVIAINTAIEADIYGNVNSTHVMGTKMMNGIGGSGDFARNA 382
>gnl|CDD|143621 cd07470, CYTH-like_mRNA_RTPase, CYTH-like mRNA triphosphatase
(RTPase) component of the mRNA capping apparatus. This
subgroup includes fungal and protozoal RTPases. RTPase
catalyzes the first step in the mRNA cap formation
process, the removal of the gamma-phosphate of
triphosphate terminated pre-mRNA. This activity is
metal-dependent. The 5'-end of the resulting mRNA
diphosphate is subsequently capped with GMP by RNA
guanylytransferase, and then further modified by one or
more methyltransferases. The mRNA cap-forming activity
is an essential step in mRNA processing. The RTPases are
not conserved among eukarya. The structure and mechanism
of this fungal RTPase domain group is different from
that of higher eukaryotes. This subgroup belongs to the
CYTH/triphosphate tunnel metalloenzyme (TTM)-like
superfamily, whose enzymes have a unique active site
located within an eight-stranded beta barrel. The RTPase
domain of the mimivirus RTPase-GTase fusion mRNA capping
enzyme also belongs to this subgroup.
Length = 243
Score = 29.3 bits (66), Expect = 0.89
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 78 NDPAIIRQNHRMTAINTCLEIDITGQVVS 106
N P + R+ R++ + ID+T +V S
Sbjct: 166 NGPILTRRKDRLSYTHNAFRIDLT-KVTS 193
>gnl|CDD|217708 pfam03743, TrbI, Bacterial conjugation TrbI-like protein. Although
not essential for conjugation, the TrbI protein greatly
increase the conjugational efficiency.
Length = 186
Score = 28.3 bits (64), Expect = 1.5
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 98 IDITGQVVSDSLGTRIYSGFGGQVD 122
ID+ G +D LG +G G+VD
Sbjct: 79 IDLPGSPGADELG---RAGIRGRVD 100
>gnl|CDD|238682 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 767
Score = 28.3 bits (63), Expect = 2.6
Identities = 29/101 (28%), Positives = 45/101 (44%), Gaps = 15/101 (14%)
Query: 76 YSNDPAIIRQNH-RMTAINTCLEIDITGQVVSDSLGT------RIYSGFGGQVDF--MRG 126
+ N + N R T I + L+ D TGQ+ S SL T R+ G+ +F
Sbjct: 136 FGNVSTALNGNATRFTQILS-LDFDQTGQIASASLQTMLLERSRVARRPNGETNFVVFSQ 194
Query: 127 ALTGLDGKGLKYQILVH---EDNSMPLLGSNPGPPDYQASA 164
L G+DG L+ ++ + E +S +G P D Q +A
Sbjct: 195 LLAGVDGD-LRTELHLEQMAESSSFG-MGGLSKPEDKQKAA 233
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.1 bits (63), Expect = 3.1
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 31 FNSGVINNSKKSIDRGQITATLLLGDKPLYDFVHNNELVQMKRGTYSNDPAIIRQNHRMT 90
+ V K+++D +L +K FV E + ++ S P I N R
Sbjct: 329 LSILVFAKDKEALDEKLAMVLNILTNK---GFVAVRETINIEPAFLSQLPGNIYYNVRKR 385
Query: 91 AINT 94
+++
Sbjct: 386 LLSS 389
>gnl|CDD|173857 cd08492, PBP2_NikA_DppA_OppA_like_15, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 484
Score = 27.6 bits (62), Expect = 3.5
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 2/43 (4%)
Query: 41 KSIDRGQITATLLLGDKPLYDFVH--NNELVQMKRGTYSNDPA 81
+IDR I T+ G P + + Y+ DP
Sbjct: 275 LAIDREAIVETVFFGSYPAASSLLSSTTPYYKDLSDAYAYDPE 317
>gnl|CDD|215701 pfam00082, Peptidase_S8, Subtilase family. Subtilases are a family
of serine proteases. They appear to have independently
and convergently evolved an Asp/Ser/His catalytic triad,
like that found in the trypsin serine proteases (see
pfam00089). Structure is an alpha/beta fold containing a
7-stranded parallel beta sheet, order 2314567.
Length = 277
Score = 27.3 bits (61), Expect = 3.9
Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 6/72 (8%)
Query: 64 HNNELVQMKRGTYSNDPAIIRQNHRMTAINTCLEIDITGQVVSDSLGTRIYSGFGGQVDF 123
E V++ G+ D + AI E +V++ SLG
Sbjct: 72 AKLESVKVLPGSGGTDSELAG------AIEWAAERPNDIRVINMSLGPVDGPPSSWSSAI 125
Query: 124 MRGALTGLDGKG 135
A+ G D KG
Sbjct: 126 DELAVNGADNKG 137
>gnl|CDD|184187 PRK13625, PRK13625, bis(5'-nucleosyl)-tetraphosphatase PrpE;
Provisional.
Length = 245
Score = 26.6 bits (59), Expect = 7.2
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 58 PLYDFVHNNELVQMKRGTYSNDPAIIRQNHRMTAINTCLEIDITGQVVSD 107
PLY + LV G + I RQ+ ++ L DITG+ D
Sbjct: 125 PLYHILDEGRLVVAHAGIRQDY--IGRQDKKVQTF--VLYGDITGEKHPD 170
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
0.318 0.138 0.404
Gapped
Lambda K H
0.267 0.0892 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,683,067
Number of extensions: 784867
Number of successful extensions: 549
Number of sequences better than 10.0: 1
Number of HSP's gapped: 544
Number of HSP's successfully gapped: 17
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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: 55 (24.7 bits)