RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy378
(107 letters)
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 29.9 bits (68), Expect = 0.20
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 13 RFRIKFPPDGNRINYVNYDKIDPFADELPKEIEDV 47
R R+ P G RI I+ + LPK +
Sbjct: 126 RLRVGLPARGRRILGR--AAINILLEALPKIVRKA 158
>gnl|CDD|222610 pfam14228, MOR2-PAG1_mid, Cell morphogenesis central region. This
family is the conserved central region of proteins that
are involved in cell morphogenesis.
Length = 1120
Score = 28.8 bits (64), Expect = 0.48
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 38 DELPKEIEDVWATLCSCWPNNMKVI 62
D+ P EIE +W+T+ S W N + V+
Sbjct: 678 DQFPDEIEKLWSTVASKWRNIVPVL 702
>gnl|CDD|199885 cd02855, E_set_GBE_prok_N, N-terminal Early set domain associated
with the catalytic domain of prokaryotic glycogen
branching enzyme. This subfamily is composed of
predominantly prokaryotic 1,4 alpha glucan branching
enzymes, also called glycogen branching enzymes. E or
"early" set domains are associated with the catalytic
domain of glycogen branching enzymes at the N-terminal
end. Glycogen branching enzyme catalyzes the formation
of alpha-1,6 branch points in either glycogen or starch
by cleavage of the alpha-1,4 glucosidic linkage,
yielding a non-reducing end oligosaccharide chain, as
well as the subsequent attachment of short glucosyl
chains to the alpha-1,6 position. By increasing the
number of non-reducing ends, glycogen is more reactive
to synthesis and digestion as well as being more
soluble. The N-terminal domain of the 1,4 alpha glucan
branching enzyme may be related to the immunoglobulin
and/or fibronectin type III superfamilies. These
domains are associated with different types of
catalytic domains at either the N-terminal or
C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase, among others.
Length = 105
Score = 27.5 bits (62), Expect = 0.90
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 6/26 (23%)
Query: 12 YRFRIKFPPDGNRINYVNYDKIDPFA 37
Y++ I+ DG + K DP+A
Sbjct: 71 YKYEIETA-DGEVL-----LKADPYA 90
>gnl|CDD|223354 COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy
production and conversion].
Length = 459
Score = 27.6 bits (61), Expect = 1.4
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 29 NYDKIDPFADELPKEIEDVWATLCSCWPNNMKVIIR 64
+ + P A PK E+V A L N + V+ R
Sbjct: 26 SVYRGLPLAVVFPKSEEEVAAILRLANENGIPVVPR 61
>gnl|CDD|205970 pfam13797, Post_transc_reg, Post-transcriptional regulator. This
family includes post-transcriptional regulators.
Length = 87
Score = 26.0 bits (58), Expect = 2.0
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 43 EIEDVWATLCS-CWPNNMKVIIRYLI--IMSGMAPNQLLNYLSMKVII 87
ED+W+ L W + L+ I+S + N+ ++YL+++
Sbjct: 29 TEEDLWSYLVEKKWKKKDPKRLHELVNDILS-LKINEYMDYLTVEAYK 75
>gnl|CDD|202493 pfam02978, SRP_SPB, Signal peptide binding domain.
Length = 101
Score = 26.3 bits (59), Expect = 2.1
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 69 MSGMAPNQLLNYLSMKVIIRYLIIMSGMAPNQLLN 103
M + P + L K + R I+ M P + N
Sbjct: 30 MGKLMPKEKNVELDEKKLKRIEAIIDSMTPKERDN 64
>gnl|CDD|226729 COG4279, COG4279, Uncharacterized conserved protein [Function
unknown].
Length = 266
Score = 25.9 bits (57), Expect = 4.5
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 10/52 (19%)
Query: 7 SDNEPYRFRIKFPP-DGNRINYVNYDKIDP--------FADELPKEIEDVWA 49
S+ EPY I P + V I + E+P+ IEDV+
Sbjct: 59 SEEEPYVVTIGIPTFSKEQWREV-IATIAQKANYAAKLLSGEMPESIEDVFV 109
>gnl|CDD|224883 COG1972, NupC, Nucleoside permease [Nucleotide transport and
metabolism].
Length = 404
Score = 26.0 bits (58), Expect = 4.5
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 65 YLIIMSGMAP---NQLLNYLSMKVIIRYLIIMSGM-APNQLL 102
+ ++ SGMA + L Y SM V YL+ S M AP LL
Sbjct: 167 FTVMASGMASVSGSILGGYASMGVPPEYLLAASFMNAPGGLL 208
>gnl|CDD|189012 cd09605, M3A, Peptidase M3A family includes Thimet oligopeptidase,
dipeptidyl carboxypeptidase and mitochondrial
intermediate peptidase. The peptidase M3-like family,
also called neurolysin-like family, is part of the
"zincins" metallopeptidases, and includes M3, M2 and M32
families of metallopeptidases. The M3 family is
subdivided into two subfamilies: the widespread M3A,
which comprises a number of high-molecular mass endo-
and exopeptidases from bacteria, archaea, protozoa,
fungi, plants and animals, and the small M3B, whose
members are enzymes primarily from bacteria. Well-known
mammalian/eukaryotic M3A endopeptidases are the thimet
oligopeptidase (TOP; endopeptidase 3.4.24.15),
neurolysin (alias endopeptidase 3.4.24.16), and the
mitochondrial intermediate peptidase. The first two are
intracellular oligopeptidases, which act only on
relatively short substrates of less than 20 amino acid
residues, while the latter cleaves N-terminal
octapeptides from proteins during their import into the
mitochondria. The M3A subfamily also contains several
bacterial endopeptidases, collectively called
oligopeptidases A, as well as a large number of
bacterial carboxypeptidases, called dipeptidyl
peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC
3.4.15.5). The peptidases in the M3 family contain the
HEXXH motif that forms the active site in conjunction
with a C-terminally-located Glutamic acid (Glu) residue.
A single zinc ion is ligated by the side-chains of the
two Histidine (His) residues, and the more C-terminal
Glu. Most of the peptidases are synthesized without
signal peptides or propeptides, and function
intracellularly. The structure of neurolysin shows
similarities to those of angiotensin-converting enzyme
(ACE; peptidyl-dipeptidase A) peptidase unit 2 belonging
to peptidase family M2. ACE is an enzyme responsible for
cleavage of dipeptides from the C-termini of proteins,
notably converting angiotensin I to angiotensin II in
mammals. There are similarities to the thermostable
carboxypeptidases from Pyrococcus furiosus
carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP),
belonging to peptidase family M32. Little is known about
function of this family, including carboxypeptidases Taq
and Pfu.
Length = 590
Score = 25.9 bits (58), Expect = 5.1
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 39 ELPKEIEDVWATLCSCWPNNMKVIIRYL 66
EL ++ + T S P+N ++ L
Sbjct: 151 ELREKRYRAYNTRGSGEPDNRALLEEIL 178
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 25.9 bits (57), Expect = 5.7
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 57 NNMKVIIRYLI 67
NNMK IRY+I
Sbjct: 690 NNMKQFIRYMI 700
>gnl|CDD|172532 PRK14038, PRK14038, ADP-dependent glucokinase; Provisional.
Length = 453
Score = 25.5 bits (56), Expect = 6.0
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 24 RINYVNYDKIDPFADELPKEIEDV 47
RI +++ +++ELPK I +
Sbjct: 46 RIEKAGKEEVLRYSEELPKRINSI 69
>gnl|CDD|219735 pfam08170, POPLD, POPLD (NUC188) domain. This domain is found in
POP1-like nucleolar proteins.
Length = 92
Score = 24.6 bits (54), Expect = 7.0
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 20 PDGNRINYVNYDKIDPFA 37
P G R+NY +PF+
Sbjct: 72 PPGKRVNYSKLGVGNPFS 89
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 0.444
Gapped
Lambda K H
0.267 0.0561 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,717,829
Number of extensions: 502870
Number of successful extensions: 485
Number of sequences better than 10.0: 1
Number of HSP's gapped: 483
Number of HSP's successfully gapped: 26
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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: 41 (22.0 bits)
S2: 53 (24.6 bits)