RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3657
(113 letters)
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 68.3 bits (168), Expect = 6e-15
Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 1 MNAIHAEKIFQFDNNTCIDSRLFSTYVDELKSLWDDVAIRQAFERRSEYQLGDSIQYFFD 60
N A+KI + L + +K LW D I+ ++RR+EYQL DS +YF D
Sbjct: 66 ENEKDAKKILSLAPRA-EEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAKYFLD 124
Query: 61 NWDRISR 67
N DRIS
Sbjct: 125 NLDRISD 131
Score = 60.2 bits (147), Expect = 4e-12
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 68 RAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHRNL 107
+ R+ K ++ HFT A DTENI+ VF+AVK+ IL NL
Sbjct: 276 LDLNRNPNKEIYPHFTCATDTENIRFVFDAVKDIILQNNL 315
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 62.6 bits (153), Expect = 7e-13
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 5 HAEKIFQFDN-NTCIDSRLFSTYVDELKSLWDDVAIRQAFERRSEYQLGDSIQYFFDNWD 63
I + N ++ L +K+LW D I++ + RR+E+QL DS YF DN D
Sbjct: 91 DIRIITEQFNKTDETENVLPKEIAKAIKALWKDEGIQECYRRRNEFQLNDSASYFLDNID 150
Query: 64 RIS 66
RI
Sbjct: 151 RIG 153
Score = 61.4 bits (150), Expect = 2e-12
Identities = 22/45 (48%), Positives = 31/45 (68%)
Query: 67 RRAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHRNLRDLM 111
R + +K ++HHFT A DT NI++VF+AVK+ IL RNL+D
Sbjct: 298 LRLNRNSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKDAG 342
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 56.9 bits (138), Expect = 7e-11
Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 2 NAIHAEKIFQFDNNTC--IDSRLFSTYVDELKSLWDDVAIRQAFERRSEYQLGDSIQYFF 59
N A+K+ ++ ++R +++K LW+D I++ + R +E+QL DS +YF
Sbjct: 71 NEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEVYNRSNEFQLSDSAKYFL 130
Query: 60 DNWDRISRR 68
DN DRI+
Sbjct: 131 DNLDRIASP 139
Score = 51.5 bits (124), Expect = 6e-09
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 64 RISRRAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHRNLRDLMLQ 113
K + ++ ++ HFT A DTEN++ VF AVK+ IL NL++ L
Sbjct: 280 NKFLELNKNNSERKIYTHFTNATDTENVRFVFEAVKDIILQNNLKESGLL 329
>gnl|CDD|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA
polymerase delta, subunit B [DNA replication,
recombination, and repair].
Length = 481
Score = 27.0 bits (60), Expect = 2.3
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 52 GDSIQYFFDNWDRISRRAVKRDEKKPLFHHFTTAVDTENIKIV--FNAVKNT 101
D + YF D ++++SR +R+E + + ++KI+ N V+ T
Sbjct: 102 EDFVPYFRDRYEKLSRIIREREEARYVSPIKKDLEGGSDVKIIGEVNDVRET 153
>gnl|CDD|238904 cd01923, cyclophilin_RING, cyclophilin_RING: cyclophilin-type
peptidylprolyl cis- trans isomerases (cyclophilins)
having a modified RING finger domain. This group
includes the nuclear proteins, Human hCyP-60 and
Caenorhabditis elegans MOG-6 which, compared to the
archetypal cyclophilin Human cyclophilin A exhibit
reduced peptidylprolyl cis- trans isomerase activity and
lack a residue important for cyclophilin binding. Human
hCyP-60 has been shown to physically interact with the
proteinase inhibitor peptide eglin c and; C. elegans
MOG-6 to physically interact with MEP-1, a nuclear zinc
finger protein. MOG-6 has been shown to function in
germline sex determination.
Length = 159
Score = 25.8 bits (57), Expect = 4.8
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 8/30 (26%)
Query: 92 KIVFNAVK--------NTILHRNLRDLMLQ 113
K N +K TI HR++R+ M+Q
Sbjct: 22 KACENFIKLCKKGYYDGTIFHRSIRNFMIQ 51
>gnl|CDD|176051 cd08406, C2B_Synaptotagmin-12, C2 domain second repeat present in
Synaptotagmin 12. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 12, a member of
class 6 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmins 8 and
13, do not have any consensus Ca2+ binding sites.
Previously all synaptotagmins were thought to be
calcium sensors in the regulation of neurotransmitter
release and hormone secretion, but it has been shown
that not all of them bind calcium. Of the 17
identified synaptotagmins only 8 bind calcium (1-3,
5-7, 9, 10). The function of the two C2 domains that
bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that
can adopt 2 structural arrangements: Type I and Type
II, distinguished by a circular permutation involving
their N- and C-terminal beta strands. Many C2 domains
are Ca2+-dependent membrane-targeting modules that bind
a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 25.5 bits (56), Expect = 5.0
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 57 YFFDNWDRISRR--AVKRDEKKPLF 79
Y + +IS++ +VKRD+ P+F
Sbjct: 43 YLLQDGRKISKKKTSVKRDDTNPIF 67
>gnl|CDD|234850 PRK00861, PRK00861, putative lipid kinase; Reviewed.
Length = 300
Score = 25.7 bits (57), Expect = 6.6
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 79 FHHFTTAVDTENIKIVFNAVKNTI 102
F ++TE+ I NAV T+
Sbjct: 170 LESFEVEIETEDQIITTNAVAVTV 193
>gnl|CDD|176455 cd01701, PolY_Rev1, DNA polymerase Rev1. Rev1 is a translesion
synthesis (TLS) polymerase found in eukaryotes.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Rev1 has both
structural and enzymatic roles. Structurally, it is
believed to interact with other nonclassical polymerases
and replication machinery to act as a scaffold.
Enzymatically, it catalyzes the specific insertion of
dCMP opposite abasic sites. Rev1 interacts with the
Rev7 subunit of the B-family TLS polymerase Pol zeta
(Rev3/Rev7). Rev1 is known to actively promote the
introduction of mutations, potentially making it a
significant target for cancer treatment.
Length = 404
Score = 25.7 bits (57), Expect = 6.8
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 18/67 (26%)
Query: 6 AEKIFQFDNNTCIDSRLFSTYVDELKS---------LW------DDVAIRQAFERRSEYQ 50
AEK+ + +TC L S ++L+ L+ DD + ER+S
Sbjct: 235 AEKLVKLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKS--- 291
Query: 51 LGDSIQY 57
+ I Y
Sbjct: 292 VSAEINY 298
>gnl|CDD|169151 PRK07912, PRK07912, salicylate synthase MbtI; Reviewed.
Length = 449
Score = 25.5 bits (56), Expect = 7.2
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 28 DELKSLWDDVAIRQAFERRSEYQLGDSI 55
DEL+ + D V RQ + R LG+++
Sbjct: 68 DELRVIRDGVTRRQQWSGRPGAALGEAV 95
>gnl|CDD|217632 pfam03599, CdhD, CO dehydrogenase/acetyl-CoA synthase delta
subunit.
Length = 384
Score = 25.6 bits (56), Expect = 7.6
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 49 YQLGDSIQYFFDNWDRISRRAVKRDE 74
LG I+ DN+ RI R A+K D+
Sbjct: 178 EALGYGIKDTIDNFVRIRRAAIKGDK 203
>gnl|CDD|185355 PRK15458, PRK15458, tagatose 6-phosphate aldolase subunit KbaZ;
Provisional.
Length = 426
Score = 25.5 bits (56), Expect = 7.7
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 7 EKIFQFDNNTCIDSRLFSTYVDELKSLWDDVAIRQAFER 45
+ + D N +R +S Y D ++ W D I AF
Sbjct: 332 QSHYHGDGNARRLARGYS-YSDRVRYYWPDSQIDDAFAH 369
>gnl|CDD|99918 cd05535, POLBc_epsilon, DNA polymerase type-B epsilon subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) epsilon has been proposed to play a
role in elongation of the leading strand during DNA
replication. Pol epsilon might also have a role in DNA
repair. The structure of pol epsilon is characteristic
of this family with the exception that it contains a
large c-terminal domain with an unclear function.
Phylogenetic analyses indicate that Pol epsilon is the
ortholog to the archaeal Pol B3 rather than to Pol
alpha, delta, or zeta. This might be because pol epsilon
is ancestral to both archaea and eukaryotes DNA
polymerases type B.
Length = 621
Score = 25.3 bits (56), Expect = 8.4
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 13/59 (22%)
Query: 53 DSIQYFFDNWDRISRRAVKRDEKKPLFHHFTTAVDTENIKIVFNAVKNTILHR--NLRD 109
D+IQ N D R A++ + K PL EN F V+ IL + +LRD
Sbjct: 35 DAIQELLQNVDETLRFAIEVEGKIPLD-------QVEN----FEEVREEILEKLQSLRD 82
>gnl|CDD|236394 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 25.4 bits (56), Expect = 9.6
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 11/80 (13%)
Query: 41 QAFERRSEYQLGDSIQYFF---DNWDRISRRAVKRDEKKPLFHH-------FTTAVDTEN 90
+ F QL +++ ++ D A+ R + L H A D +
Sbjct: 788 RTFTMAGLAQLANAMARLILKLEDQDDEEDLALARARLRELAAHLDLRPERLEQA-DARD 846
Query: 91 IKIVFNAVKNTILHRNLRDL 110
I ++F A+ + L LR L
Sbjct: 847 IAVLFKALASARLKDGLRLL 866
>gnl|CDD|187814 cd09683, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily
protein Csm3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 216
Score = 25.2 bits (55), Expect = 9.6
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 7/46 (15%)
Query: 7 EKIFQFDNNTCIDSRLFSTYVDELKSLWDDVAIRQAFERRSEYQLG 52
+ + F N TC+ LF + L V I A E
Sbjct: 97 DALETFWNKTCLPCILFGS-----PWLASRVYILDA--VAEEPSDQ 135
>gnl|CDD|178124 PLN02508, PLN02508, magnesium-protoporphyrin IX monomethyl ester
[oxidative] cyclase.
Length = 357
Score = 25.1 bits (55), Expect = 9.6
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 22 LFSTYVDELKSLWDDVAIRQAFERRSEYQLGDSIQYFFDNW 62
++TY+ E W + I + + +YQL +Y F+NW
Sbjct: 161 FYATYLSEKIGYWRYITIYRHLQANPDYQLYPIFKY-FENW 200
>gnl|CDD|233938 TIGR02581, cas_cyan_RAMP, CRISPR-associated RAMP protein, SSO1426
family. Members of this CRISPR-associated (cas) gene
family are found in the RAMP-2 subtype of CRISPR/cas
locus and designated TM1809 family [Mobile and
extrachromosomal element functions, Other].
Length = 217
Score = 25.2 bits (55), Expect = 9.7
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 7/46 (15%)
Query: 7 EKIFQFDNNTCIDSRLFSTYVDELKSLWDDVAIRQAFERRSEYQLG 52
+ + F N TC+ LF + L V I A E
Sbjct: 97 DALETFWNKTCLPCILFGS-----PWLASRVYILDA--VAEEPSDQ 135
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
0.325 0.137 0.411
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,839,348
Number of extensions: 499231
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 34
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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: 40 (21.6 bits)
S2: 53 (24.1 bits)