RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12319
(161 letters)
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 40.7 bits (96), Expect = 8e-05
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 84 QLSTDEVNLVANEKYRKKREQEVSREGYQFHINSVSKIDRVSRILFPASFGLLNLFYW 141
+ + + V +A + EV + IDR+SR +FP +F L L YW
Sbjct: 175 KKALEGVRFIAEHLRSRDEFDEVKEDWKY----VAMVIDRLSRWIFPIAFVLGTLVYW 228
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 39.7 bits (93), Expect = 3e-04
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 102 REQEVSREGYQFHINSVSKIDRVSRILFPASFGLLNLFYWISY 144
R+++ S E + ID++SR+ FP +F L N+ YW+SY
Sbjct: 417 RKRDESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIGYWMSY 459
>gnl|CDD|238070 cd00123, DmpA_OAT, DmpA/OAT superfamily; composed of
L-aminopeptidase D-amidase/D-esterase (DmpA), ornithine
acetyltransferase (OAT) and similar proteins. DmpA is an
aminopeptidase that releases N-terminal D and L amino
acids from peptide substrates. This group represents one
of the rare aminopeptidases that are not metalloenzymes.
DmpA shows similarity in catalytic mechanism to
N-terminal nucleophile (Ntn) hydrolases, which are
enzymes that catalyze the cleavage of amide bonds
through the nucleophilic attack of the side chain of an
N-terminal serine, threonine, or cysteine. OAT catalyzes
the first and fifth steps in arginine biosynthesis,
coupling acetylation of glutamate with deacetylation of
N-acetylornithine, which allows recycling of the acetyl
group in the arginine biosynthetic pathway. The
superfamily also contains an enzyme, endo-type
6-aminohexanoate-oligomer hydrolase, that have been
shown to be involved in nylon degradation. Proteins in
this superfamily undergo autocatalytic cleavage of an
inactive precursor at the site immediately upstream to
the catalytic nucleophile.
Length = 286
Score = 29.7 bits (66), Expect = 0.55
Identities = 9/40 (22%), Positives = 14/40 (35%)
Query: 13 FAAVHYFTKTGSGEIPFLVSSDEIRVHPHPKSYVSEDEED 52
F V T T +G+ ++ + P S E D
Sbjct: 227 FNRVSIDTDTSTGDTAVAFATGLAGLPTTPGSSRGRLEVD 266
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 27.4 bits (61), Expect = 4.4
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 14/46 (30%)
Query: 91 NLVANEKYRKKR------EQEVSR----EGYQFHINSVSKIDRVSR 126
LVAN RK + E E+S+ GY + IN ID +R
Sbjct: 327 ELVANPNIRKTKIKARDLETEISKLQQESGYPYIIN----IDTANR 368
>gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein. Hemolysins are
exotoxins that attack blood cell membranes and cause
cell rupture, often by forming a pore in the membrane.
At least two members of this protein family have been
characterized indirectly as pore-forming hemolysins, one
from the spirochete Serpula (Treponema) hyodysenteriae
and one from Mycobacterium tuberculosis. However,
homology domains in this protein suggest
methyltransferase activity (pfam01728) and RNA-binding
activity (pfam01479) [Unknown function, General].
Length = 228
Score = 27.1 bits (60), Expect = 4.4
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 53 EQTNIH-----KIKVDYRVCSVYEIRTLKVCPNIVDQLSTDEVNLVANEKYRKKRE 103
E+TNI I D+ V I + + P + L+ +++ L+ ++ RE
Sbjct: 125 ERTNIRYVTPADIFPDFATFDVSFISLISILPELDLLLNPNDLTLLFKPQFEAGRE 180
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal
regulatory protein Rpn11 and signalosome complex subunit
CSN5. This family contains proteasomal regulatory
protein Rpn11 (26S proteasome regulatory subunit rpn11;
PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the
19S-proteasome; regulatory particle number 11) and
signalosomal CSN5 (COP9 signalosome complex subunit 5;
COP9 complex homolog subunit 5; c-Jun activation
domain-binding protein-1; CSN5/JAB1; JAB1). COP9
signalosome (CSN) and the proteasome lid are paralogous
complexes and their respective subunits CSN5 and Rpn11
are most closely related between the two complexes, both
containing the conserved JAMM (JAB1/MPN/Mov34
metalloenzyme) motif involved in zinc ion coordination
and providing the active site for isopeptidase activity.
Rpn11 is responsible for substrate deubiquitination
during proteasomal degradation. It is essential for
maintaining a correct cell cycle and normal
mitochondrial morphology and physiology; mutations in
Rpn11 cause cell cycle and mitochondrial defects,
temperature sensitivity and sensitivity to DNA damaging
reagents such as UV. It has been shown that the
C-terminal region of Rpn11 is involved in the regulation
of the mitochondrial fission and tubulation processes.
CSN5, one of the eight subunits of CSN, is critical for
nuclear export and the degradation of several tumor
suppressor proteins, including p53, p27, and Smad4. Its
MPN+ domain is critical for the physical interaction of
RUNX3 and Jab1. It has been suggested that the direct
interaction of CSN5/JAB1 with p27 provides p27 with a
leucine-rich nuclear export signal (NES), which is
required for binding to chromosomal region maintenance 1
(CRM1), and facilitates nuclear export. The
over-expression of CSN5/JAB1 also has been implicated in
cancer initiation and progression, including cancer of
the lung, pancreas, mouth, thyroid, and breast,
suggesting that the oncogenic activity of CSN5 is
associated with the down-regulation of RUNX3.
Length = 268
Score = 26.8 bits (60), Expect = 5.6
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 72 IRTLKVCPNIV-DQLSTDEVNLVANEKYRKKREQEVSREGYQFHINSVSKIDRVS 125
+ TL + P + T + L EK K +QE G + I +V K+D+
Sbjct: 205 VNTLSLSPLLENSNEYTIKQILDLAEKLEKAEQQEERLTGEELDIANVGKLDKAR 259
>gnl|CDD|235942 PRK07119, PRK07119, 2-ketoisovalerate ferredoxin reductase;
Validated.
Length = 352
Score = 26.7 bits (60), Expect = 6.8
Identities = 15/39 (38%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 79 PNIVDQLSTD-----EVNLVANEKYRKKREQEVSREGYQ 112
NI+ L D + NL EKY K E EV E Y
Sbjct: 205 KNIITSLFLDPEELEKHNLRLQEKYAKIEENEVRYEEYN 243
>gnl|CDD|221594 pfam12476, DUF3696, Protein of unknown function (DUF3696). This
domain family is found in bacteria and archaea, and is
approximately 50 amino acids in length.
Length = 52
Score = 24.2 bits (53), Expect = 9.4
Identities = 8/33 (24%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 31 VSSDEIRVHPHPKSYVSEDEEDEQTNIHKIKVD 63
+ D++ ++ Y DEE+ ++ + +IK+D
Sbjct: 1 IDPDDVALY-----YFERDEEEGESEVREIKID 28
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 26.1 bits (58), Expect = 9.4
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 115 INSVSKIDRVSRILFPASFGLLNL 138
+N +S D V +F AS+ +L L
Sbjct: 932 VNGLSSRDDVRDTVFDASYLVLGL 955
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 26.4 bits (58), Expect = 9.6
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 80 NIVDQLSTDEVNLVANEKYRKKREQEVSREGYQFHINSVSKIDRVSRILFPASFGLLNLF 139
N +D S + NLV N YR + Y+F I +K DR +++ P + + NL
Sbjct: 556 NQIDPNSKEPQNLV-NTDYRTYNFDVIDGVTYKFDITQPNKYDRDGKLVNPTASRVRNLQ 614
Query: 140 YWISYITDQENFV 152
Y + + F+
Sbjct: 615 YNGQPVDANQEFI 627
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
0.321 0.136 0.409
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,204,722
Number of extensions: 722970
Number of successful extensions: 595
Number of sequences better than 10.0: 1
Number of HSP's gapped: 595
Number of HSP's successfully gapped: 21
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (24.9 bits)