RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2215
(172 letters)
>gnl|CDD|100049 cd03359, LbH_Dynactin_5, Dynactin 5 (or subunit p25); Dynactin is a
major component of the activator complex that stimulates
dynein-mediated vesicle transport. Dynactin is a
heterocomplex of at least eight subunits, including a
150,000-MW protein called Glued, the actin-capping
protein Arp1, and dynamatin. In vitro binding
experiments show that dynactin enhances dynein-dependent
motility, possibly through interaction with microtubules
and vesicles. Subunit p25 is part of the pointed-end
subcomplex in dynactin that also includes p26, p27, and
Arp11. This subcomplex interacts with membranous
cargoes. p25 and p27 contain imperfect tandem repeats of
a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X),
indicating a left-handed parallel beta helix (LbH)
structural domain. Proteins containing hexapeptide
repeats are often enzymes showing acyltransferase
activity.
Length = 161
Score = 111 bits (279), Expect = 1e-31
Identities = 54/96 (56%), Positives = 67/96 (69%), Gaps = 7/96 (7%)
Query: 67 ASGNKVSRKSLVAGAQNIVLTGKVIIQCDAVLRGDLANIRTGRYCIISKGVVIRPPFKKF 126
ASGNKVSRKS++ G+QNIVL GK IIQ D ++RGDLA + GRYCI+S+G VIRPPFKKF
Sbjct: 5 ASGNKVSRKSVICGSQNIVLNGKTIIQSDVIIRGDLATVSIGRYCILSEGCVIRPPFKKF 64
Query: 127 AKGFLVYP---GSTVYLVFTASVRLKSPFAQIYSYI 159
+KG +P G V++ V AQI SY+
Sbjct: 65 SKGVAFFPLHIGDYVFIGENCVVNA----AQIGSYV 96
>gnl|CDD|223735 COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine
patch superfamily [General function prediction only].
Length = 176
Score = 41.0 bits (97), Expect = 5e-05
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 81 AQNIVLTGKVIIQCD------AVLRGDLANIRTGRYCIISKGVVIR 120
A + + G V I AVLRGD+ IR G I GVVI
Sbjct: 21 APSATVIGDVRIGAGVSIWPGAVLRGDVEPIRIGARTNIQDGVVIH 66
>gnl|CDD|237304 PRK13206, ureC, urease subunit alpha; Reviewed.
Length = 573
Score = 33.9 bits (78), Expect = 0.035
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 65 AVASGNKVSRKSL-------VAGAQNIVLTGKVIIQCDAVLRGDLANIRTGRYCIISK 115
AV G KV R+S+ GA + V+TG VI+ +++ D+ IR GR I K
Sbjct: 47 AVFGGGKVIRESMGQGRATRAEGAPDTVITGAVILDHWGIVKADVG-IRDGRIVAIGK 103
>gnl|CDD|100051 cd04645, LbH_gamma_CA_like, Gamma carbonic anhydrase-like: This
family is composed of gamma carbonic anhydrase (CA),
Ferripyochelin Binding Protein (FBP), E. coli paaY
protein, and similar proteins. CAs are zinc-containing
enzymes that catalyze the reversible hydration of carbon
dioxide in a two-step mechanism, involving the
nucleophilic attack of a zinc-bound hydroxide ion on
carbon dioxide, followed by the regeneration of the
active site by ionization of the zinc-bound water
molecule and removal of a proton from the active site.
They are ubiquitous enzymes involved in fundamental
processes like photosynthesis, respiration, pH
homeostasis and ion transport. There are three
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Gamma CAs are
trimeric enzymes with left-handed parallel beta helix
(LbH) structural domain.
Length = 153
Score = 30.5 bits (70), Expect = 0.23
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 81 AQNIVLTGKVIIQCD------AVLRGDLANIRTGRYCIISKGVVIR 120
A N + G V + AVLRGD+ IR G I G V+
Sbjct: 9 APNATVIGDVTLGEGSSVWFGAVLRGDVNPIRIGERTNIQDGSVLH 54
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 29.6 bits (66), Expect = 0.87
Identities = 14/32 (43%), Positives = 23/32 (71%), Gaps = 2/32 (6%)
Query: 77 LVAGAQNIVLTGKVIIQCDAV--LRGDLANIR 106
++AGAQ++ LTG +++ AV L GD A++R
Sbjct: 451 VLAGAQSMALTGDIVVDDGAVLSLEGDAADLR 482
>gnl|CDD|234433 TIGR03992, Arch_glmU, UDP-N-acetylglucosamine
diphosphorylase/glucosamine-1-phosphate
N-acetyltransferase. The MJ_1101 protein from
Methanococcus jannaschii has been characterized as the
GlmU enzyme catalyzing the final two steps of UDP-GlcNAc
biosynthesis. Many of the genes identified by this model
are in proximity to the GlmS and GlmM genes and are also
presumed to be GlmU. However, some archaeal genomes
contain multiple closely-related homologs from this
family and it is not clear what the substrate
specificity is for each of them.
Length = 393
Score = 29.1 bits (66), Expect = 1.2
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 11/43 (25%)
Query: 83 NIVLTGKVIIQCDAVLRGDLANIRTGRY----CIISKGVVIRP 121
N+ + G V+I G+ A IR+G Y I K I P
Sbjct: 242 NVTIKGPVVI-------GEGAVIRSGTYIEGPVYIGKNCDIGP 277
>gnl|CDD|171613 PRK12621, flgB, flagellar basal body rod protein FlgB; Provisional.
Length = 136
Score = 27.8 bits (62), Expect = 1.7
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 75 KSLVAGAQNIVLTGKVI---IQCDAVLRGDLANIRTGRY 110
KSL +I L GKV+ +Q V+ +LAN+ T Y
Sbjct: 2 KSLFE--SHINLVGKVMDMQLQRQNVVMSNLANVNTPGY 38
>gnl|CDD|132284 TIGR03240, arg_catab_astD, succinylglutamic semialdehyde
dehydrogenase. Members of this protein family are
succinylglutamic semialdehyde dehydrogenase (EC
1.2.1.71), the fourth enzyme in the arginine
succinyltransferase (AST) pathway for arginine
catabolism [Energy metabolism, Amino acids and amines].
Length = 484
Score = 27.4 bits (61), Expect = 3.9
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 10/47 (21%)
Query: 7 YYDRDSYVET------VSSGQRCLLANTNRRVWVQSQPSGAVDFLSR 47
D D+ V +S+GQRC A RR+ V G FL+R
Sbjct: 253 VADIDAAVHLIIQSAFISAGQRCTCA---RRLLVPDGAQGDA-FLAR 295
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 27.0 bits (61), Expect = 4.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 96 AVLRGDLANIRTGR 109
L+ +LA IRTGR
Sbjct: 18 EALKRELAKIRTGR 31
>gnl|CDD|220962 pfam11066, DUF2867, Protein of unknown function (DUF2867). This
bacterial family of proteins have no known function.
Length = 146
Score = 26.5 bits (59), Expect = 6.1
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 130 FLVYPGSTVYLVFTASVRLKSPFAQIYSYIIAP 162
V + T VR + ++Y + P
Sbjct: 104 VDVQDDGAGRVSMTTLVRTHNLLGRLYLAAVLP 136
>gnl|CDD|234846 PRK00844, glgC, glucose-1-phosphate adenylyltransferase;
Provisional.
Length = 407
Score = 26.7 bits (60), Expect = 6.9
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 72 VSRKSLVAGAQ--NIVLTGKVIIQCDAVLRGD--LANIRTGRYC-----IISKGVVIRP 121
VS S+++GA N VL+ V+++ A + + +R GR I+ K VV+ P
Sbjct: 318 VSAGSIISGATVRNSVLSPNVVVESGAEVEDSVLMDGVRIGRGAVVRRAILDKNVVVPP 376
>gnl|CDD|222044 pfam13320, DUF4091, Domain of unknown function (DUF4091). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, archaea and
eukaryotes, and is approximately 70 amino acids in
length. There is a single completely conserved residue G
that may be functionally important.
Length = 67
Score = 24.8 bits (55), Expect = 7.9
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 129 GFLVYPGSTVYLVFTASVRLKS 150
GFLVYPG V +S+RL+
Sbjct: 32 GFLVYPGEDGKPV--SSLRLEV 51
>gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter
ATP-binding subunit. This model describes daunorubicin
resistance ABC transporter, ATP binding subunit in
bacteria and archaea. This model is restricted in its
scope to preferentially recognize the ATP binding
subunit associated with effux of the drug, daunorubicin.
This transport system belong to the larger ATP-Binding
Cassette (ABC) transporter superfamily. The
characteristic feature of these transporter is the
obligatory coupling of ATP hydrolysis to substrate
translocation. The minimal configuration of bacterial
ABC transport system: an ATPase or ATP binding subunit;
An integral membrane protein; a hydrophilic polypetpide,
which likely functions as substrate binding protein. In
eukaryotes proteins of similar function include p-gyco
proteins, multidrug resistance protein etc [Transport
and binding proteins, Other].
Length = 302
Score = 26.6 bits (59), Expect = 8.0
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 1 MELSNIYYDRDSYVETVSSGQR 22
+EL + D V T S G R
Sbjct: 109 LELFELGEAADRPVGTYSGGMR 130
>gnl|CDD|143414 cd07095, ALDH_SGSD_AstD, N-succinylglutamate 5-semialdehyde
dehydrogenase, AstD-like. N-succinylglutamate
5-semialdehyde dehydrogenase or succinylglutamic
semialdehyde dehydrogenase (SGSD, E. coli AstD,
EC=1.2.1.71) involved in L-arginine degradation via the
arginine succinyltransferase (AST) pathway and catalyzes
the NAD+-dependent reduction of succinylglutamate
semialdehyde into succinylglutamate.
Length = 431
Score = 26.5 bits (59), Expect = 8.8
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 18/80 (22%)
Query: 17 VSSGQRCLLANTNRRVWVQSQPSGAV--DFLSR----------GWWFESKSSHKILVYSG 64
+++GQRC A RR+ V P GAV FL R G L+ +
Sbjct: 234 LTAGQRCTCA---RRLIV---PDGAVGDAFLERLVEAAKRLRIGAPDAEPPFMGPLIIAA 287
Query: 65 AVASGNKVSRKSLVAGAQNI 84
A A + L G + +
Sbjct: 288 AAARYLLAQQDLLALGGEPL 307
>gnl|CDD|189010 cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N. This
family contains mostly bacterial and some archaeal
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN consists of a
small N-terminal cytoplasmic domain, a single
transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and, in higher eukaryotes,
is present in a variety of human tissues and cell types
(leukocyte, fibroblast, endothelial and epithelial
cells). APN expression is dysregulated in inflammatory
diseases such as chronic pain, rheumatoid arthritis,
multiple sclerosis, systemic sclerosis, systemic lupus
erythematosus, polymyositis/dermatomyosytis and
pulmonary sarcoidosis, and is enhanced in tumor cells
such as melanoma, renal, prostate, pancreas, colon,
gastric and thyroid cancers. It is predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 415
Score = 26.4 bits (59), Expect = 9.8
Identities = 18/61 (29%), Positives = 22/61 (36%), Gaps = 16/61 (26%)
Query: 27 NTNRRVWVQSQPSGAVDFLSRGWWFESK--SSHK------ILVYSG--AVASGNKVSRKS 76
VW QP GA WF S K + V +G V++G VSR
Sbjct: 102 EGPDGVWTAGQPEGAS------TWFPCNDHPSDKATFDISVTVPAGYTVVSNGRLVSRTD 155
Query: 77 L 77
L
Sbjct: 156 L 156
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
0.323 0.136 0.424
Gapped
Lambda K H
0.267 0.0818 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,492,210
Number of extensions: 761034
Number of successful extensions: 586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 583
Number of HSP's successfully gapped: 29
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)