RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17978
(174 letters)
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This region
is found C-terminal to the dynein heavy chain N-terminal
region 1 (pfam08385) in many members of this family. No
functions seem to have been attributed specifically to
this region.
Length = 408
Score = 141 bits (357), Expect = 8e-41
Identities = 47/115 (40%), Positives = 76/115 (66%), Gaps = 1/115 (0%)
Query: 53 KIETTWKNLEFTCIPHRDSKNVFILAGLEEVQTILDESLISLATILSSRQVAQIRESAEQ 112
KI+ TW+ LEF +P++D ++L G +E+ +LD++L++L ++ +S V E A++
Sbjct: 150 KIKDTWEELEFELVPYKD-TGTYLLKGWDEIIELLDDNLVTLQSMKASPYVKPFEEEADE 208
Query: 113 WRQMLFLFSKTLDEWINFQNNWLYLESIFTGPDIQKQLPNESKLFTEVDKFWKRI 167
W + L L + L+ W+ Q W+YLE IF+ DI+KQLP ESK F+ VDK WK++
Sbjct: 209 WEKKLNLIQEVLELWLKVQRKWVYLEPIFSSSDIKKQLPEESKRFSNVDKEWKKL 263
>gnl|CDD|216372 pfam01223, Endonuclease_NS, DNA/RNA non-specific endonuclease.
Length = 157
Score = 34.3 bits (79), Expect = 0.013
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 16/76 (21%)
Query: 109 SAEQWRQMLFLFSKTLDEWINF-QNNWLYLES-------------IFTGPDIQKQLPNES 154
S + F ++ +W F + NW YLE+ ++TGP LP
Sbjct: 76 STSAQKA-TFYYTNMAPQWAGFNRGNWAYLENYVRDLARKNRDVYVYTGPLGVPTLPTLG 134
Query: 155 KLFTEVDK-FWKRIDF 169
V FW +DF
Sbjct: 135 NNKVAVPTHFWTGLDF 150
>gnl|CDD|225046 COG2135, COG2135, Uncharacterized conserved protein [Function
unknown].
Length = 226
Score = 32.4 bits (74), Expect = 0.073
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 68 HRDSKNVFILAGLEEVQTILDESLISLATILSSRQVAQIRESAEQWRQMLFLFSKTLDEW 127
R +F AGL E + TIL++ + + R + L + D W
Sbjct: 122 RRKDGALFFFAGLWETWFEAGGDELESFTILTTEANDLLAPIHD--RMPVVLAPEDWDAW 179
Query: 128 INFQNNWLYLESIFTGPD 145
++ L+ +
Sbjct: 180 LD-PKTPPELKELLRPLP 196
>gnl|CDD|133381 cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the
transcription regulators TipAL, Mta, and SkgA.
Helix-turn-helix (HTH) TipAL, Mta, and SkgA
transcription regulators, and related proteins,
N-terminal domain. TipAL regulates resistance to and
activation by numerous cyclic thiopeptide antibiotics,
such as thiostrepton. Mta is a global transcriptional
regulator; the N-terminal DNA-binding domain of Mta
interacts directly with the promoters of mta, bmr, blt,
and ydfK, and induces transcription of these
multidrug-efflux transport genes. SkgA has been shown to
control stationary-phase expression of
catalase-peroxidase in Caulobacter crescentus. These
proteins are comprised of distinct domains that harbor
an N-terminal active (DNA-binding) site and a
regulatory (effector-binding) site. The conserved
N-terminal domain of these transcription regulators
contains winged HTH motifs that mediate DNA binding.
These proteins share the N-terminal DNA binding domain
with other transcription regulators of the MerR
superfamily that promote transcription by reconfiguring
the spacer between the -35 and -10 promoter elements.
Unique to this family, is a TipAL-like, lineage specific
Bacilli subgroup, which has five conserved cysteines in
the C-terminus of the protein.
Length = 103
Score = 27.1 bits (61), Expect = 2.3
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 80 LEEVQTILDESLISLATILSSRQVAQIRESAEQWRQMLFLFSKTLDE 126
L+E++ +L + L L Q + E E+ +++ KT+D
Sbjct: 60 LKEIKELLKDPSEDLLEAL-REQKELLEEKKERLDKLI----KTIDR 101
>gnl|CDD|217943 pfam04180, LTV, Low temperature viability protein. The
low-temperature viability protein LTV1 is involved in
ribosome biogenesis 40S subunit production.
Length = 426
Score = 27.3 bits (60), Expect = 5.5
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 73 NVFILAGLEEVQTILDESLISLATILSSRQVAQIRESAEQWRQML 117
NV ++ + +LDE L S + R+ A+ RE + + L
Sbjct: 367 NVLAKKTAKQFERMLDEFLGSYLPKVQGRKKAKKREDKRKRKSAL 411
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 25.1 bits (56), Expect = 5.8
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 88 DESLISLATILSSRQVAQIRESAEQWRQMLFLFSKTLDEWI 128
DE + IL+SR AQ++ + +++ + K L++ I
Sbjct: 3 DEKTL--IEILASRSNAQLQAIKQAYKKR---YGKDLEDDI 38
>gnl|CDD|238043 cd00091, NUC, DNA/RNA non-specific endonuclease; prokaryotic and
eukaryotic double- and single-stranded DNA and RNA
endonucleases also present in phosphodiesterases. They
exists as monomers and homodimers.
Length = 241
Score = 26.9 bits (60), Expect = 6.0
Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 16/51 (31%)
Query: 109 SAEQWRQMLFLFSKTLDEWINF-QNNWLYLE--------------SIFTGP 144
S + F + + F Q NW YLE + TGP
Sbjct: 91 SQDAQDA-TFYLTNMAPQVQGFNQGNWAYLEDYLRDLAASEGKDVYVVTGP 140
>gnl|CDD|189000 cd08662, M13, Peptidase family M13 includes neprilysin,
endothelin-converting enzyme I. M13 family of
metallopeptidases includes neprilysin (neutral
endopeptidase, NEP, enkephalinase, CD10, CALLA, EC
3.4.24.11), endothelin-converting enzyme I (ECE-1, EC
3.4.24.71), erythrocyte surface antigen KELL (ECE-3),
phosphate-regulating gene on the X chromosome (PHEX),
soluble secreted endopeptidase (SEP), and damage-induced
neuronal endopeptidase (DINE)/X-converting enzyme (XCE).
These proteins consist of a short N-terminal cytoplasmic
domain, a single transmembrane helix, and a larger
C-terminal extracellular domain containing the active
site. Proteins in this family fulfill a broad range of
physiological roles due to the greater variation in the
S2' subsite allowing substrate specificity. NEP is
expressed in a variety of tissues including kidney and
brain, and is involved in many physiological and
pathological processes, including blood pressure and
inflammatory response. It degrades a wide array of
substrates such as substance P, enkephalins,
cholecystokinin, neurotensin and somatostatin. It is an
important enzyme in the regulation of amyloid-beta
(Abeta) protein that forms amyloid plaques that are
associated with Alzeimers disease (AD). ECE-1 catalyzes
the final rate-limiting step in the biosynthesis of
endothelins via post-translational conversion of the
biologically inactive big endothelins. Like NEP, it also
hydrolyses bradykinin, substance P, neurotensin and
Abeta. Endothelin-1 overproduction has been implicated
in various diseases, including stroke, asthma,
hypertension, and cardiac and renal failure. Kell is a
homolog of NEP and constitutes a major antigen on human
erythrocytes; it preferentially cleaves big endothelin-3
to produce bioactive endothelin-3, but is also known to
cleave substance P and neurokinin A. PHEX forms a
complex interaction with fibroblast growth factor 23
(FGF23) and matrix extracellular phosphoglycoprotein,
causing bone mineralization. A loss-of-function mutation
in PHEX disrupts this interaction leading to
hypophosphatemic rickets; X-linked hypophosphatemic
(XLH) rickets is the most common form of metabolic
rickets. ECEL1 is a brain metalloprotease involved in
the critical role in the nervous regulation of the
respiratory system, while DINE (damage induced neuronal
endopeptidase) is abundantly expressed in the
hypothalamus and its expression responds to nerve injury
as well. Thus, majority of these M13 proteases are prime
therapeutic targets for selective inhibition.
Length = 611
Score = 26.9 bits (60), Expect = 6.2
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 101 RQVAQIRESAEQWRQMLFLFSK-TLDE----WINFQNNWL-YLESIFTGPDIQKQLPNES 154
++A+I S E+ R ++ TL E +W YLE++ + +K + +
Sbjct: 162 TELAKISWSEEERRDPEKTYNPMTLAELQKLAPGI--DWKAYLEALGLPSEDEKVIVTQP 219
Query: 155 KLFTEVDKFWKRIDFRRLK 173
+++K R LK
Sbjct: 220 DYLKKLNKLLASTPLRTLK 238
>gnl|CDD|214845 smart00835, Cupin_1, Cupin. This family represents the conserved
barrel domain of the 'cupin' superfamily ('cupa' is the
Latin term for a small barrel). This family contains 11S
and 7S plant seed storage proteins, and germins. Plant
seed storage proteins provide the major nitrogen source
for the developing plant.
Length = 146
Score = 26.1 bits (58), Expect = 6.5
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 60 NLEFTCIPHRDSKNVFILAGLEEVQTILDESLISLATILSSRQV 103
NLEF D F LAG V L +++ A +S+ +V
Sbjct: 102 NLEFVAFNTNDPNRRFFLAGRNSVLRGLPPEVLAAAFGVSAEEV 145
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 26.4 bits (59), Expect = 8.3
Identities = 12/56 (21%), Positives = 18/56 (32%), Gaps = 4/56 (7%)
Query: 78 AGLEEVQTILDESLISLATILSSRQVAQIRESAEQ----WRQMLFLFSKTLDEWIN 129
E + +SL +L V I E E +L + LD+ I
Sbjct: 91 LLKELAAQFDLAAELSLDDLLRLPGVLAIEEEEEDLEALEALILAALEEALDDLIE 146
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 26.0 bits (58), Expect = 8.7
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 72 KNVFILAGLEEVQTILDESLISLATILSSRQVAQIR----ESAEQWRQM 116
+N+ I+A ++ +T L +SL++ A I+S + + R EQ R +
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGI 49
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
0.319 0.135 0.409
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,894,505
Number of extensions: 792095
Number of successful extensions: 730
Number of sequences better than 10.0: 1
Number of HSP's gapped: 729
Number of HSP's successfully gapped: 24
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)