RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8055
(139 letters)
>gnl|CDD|215647 pfam00002, 7tm_2, 7 transmembrane receptor (Secretin family). This
family is known as Family B, the secretin-receptor
family or family 2 of the G-protein-coupled receptors
(GCPRs).They have been described in many animal species,
but not in plants, fungi or prokaryotes. Three distinct
sub-families are recognised. Subfamily B1 contains
classical hormone receptors, such as receptors for
secretin and glucagon, that are all involved in
cAMP-mediated signalling pathways. Subfamily B2 contains
receptors with long extracellular N-termini, such as the
leukocyte cell-surface antigen CD97 ;
calcium-independent receptors for latrotoxin, and
brain-specific angiogenesis inhibitors amongst others.
Subfamily B3 includes Methuselah and other Drosophila
proteins. Other than the typical seven-transmembrane
region, characteristic structural features include an
amino-terminal extracellular domain involved in ligand
binding, and an intracellular loop (IC3) required for
specific G-protein coupling.
Length = 239
Score = 101 bits (255), Expect = 9e-28
Identities = 42/89 (47%), Positives = 62/89 (69%), Gaps = 1/89 (1%)
Query: 50 TMIYSVGYTLSLIALIIAVWIFVYFKDLRCLRNKIHTNLMCTYILADFMWIL-TMTVQMS 108
+IY+VGY+LSL+AL++A+ IF+ F+ LRC RN IH NL ++IL ++++ + S
Sbjct: 5 KVIYTVGYSLSLVALLLAIAIFLLFRKLRCTRNYIHLNLFASFILRAILFLVGDAVLFNS 64
Query: 109 VQSNFACVILYIFLHYCHLTNFFWMFVEG 137
V S+ C ++ +FLHY L NFFWM VEG
Sbjct: 65 VGSDVVCKVVAVFLHYFFLANFFWMLVEG 93
>gnl|CDD|202399 pfam02793, HRM, Hormone receptor domain. This extracellular
domain contains four conserved cysteines that probably
for disulphide bridges. The domain is found in a
variety of hormone receptors. It may be a ligand
binding domain.
Length = 63
Score = 30.8 bits (70), Expect = 0.046
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 3 LFFYLNAENASKWCNANGSWNS-FANYSLCTDI 34
+ + NAS+ C NG+W+ NYS CT
Sbjct: 31 FYDFDPTGNASRNCTENGTWSEHPPNYSNCTSN 63
>gnl|CDD|114045 pfam05297, Herpes_LMP1, Herpesvirus latent membrane protein 1
(LMP1). This family consists of several latent membrane
protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1
of EBV is a 62-65 kDa plasma membrane protein possessing
six membrane spanning regions, a short cytoplasmic
N-terminus and a long cytoplasmic carboxy tail of 200
amino acids. EBV latent membrane protein 1 (LMP1) is
essential for EBV-mediated transformation and has been
associated with several cases of malignancies. EBV-like
viruses in Cynomolgus monkeys (Macaca fascicularis) have
been associated with high lymphoma rates in
immunosuppressed monkeys.
Length = 382
Score = 31.1 bits (70), Expect = 0.14
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 55 VGYTLSLIALIIAVWIFVYFKDLRCLRNKIHTNLMCTYILADFMWILTMTVQMSVQSNFA 114
V Y+ +LI +II + IF++ +DL C + L+ +L +W + Q+ +
Sbjct: 54 VLYSFALILIIIILIIFIFRRDLLCPLGALCLLLLMITLLLIALW------NLHGQALYL 107
Query: 115 CVILYIFLHYCHLTNFFWMFV 135
++L+IF C L W+++
Sbjct: 108 GIVLFIF--GCLLVLGLWIYL 126
Score = 27.3 bits (60), Expect = 2.8
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 64 LIIAVWIFVYFKDLRCLRNKIHTNLMCTYILADFMWILTMTVQMSVQSNFACVILYIFLH 123
L++ +WI++ + L L I + + LA F+ I+ + + + +Q N+ +++ +
Sbjct: 118 LVLGLWIYL-LEILWRLGATIWQ--LLAFFLAFFLAIILLIIALYLQQNWWTLLVDLLWL 174
Query: 124 YCHLTNFFWMFVEGSR 139
L WM+ G R
Sbjct: 175 LLFLAILIWMYYHGPR 190
>gnl|CDD|214468 smart00008, HormR, Domain present in hormone receptors.
Length = 70
Score = 27.9 bits (62), Expect = 0.49
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 8 NAENASKWCNANGSW-NSFANYSLCT 32
AS+ C NG W F NYS CT
Sbjct: 37 YKTGASRNCTENGGWSPPFPNYSNCT 62
>gnl|CDD|237550 PRK13899, PRK13899, type IV secretion system protein VirB3;
Provisional.
Length = 97
Score = 27.8 bits (62), Expect = 1.0
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 50 TMIYSVGYTLSLIALIIAVWIFVYFKDLRCL 80
MI+ V Y + + +II++ +F++ D R L
Sbjct: 18 PMIFGVSYKFAALNMIISMMVFIWTNDFRIL 48
>gnl|CDD|227333 COG5000, NtrY, Signal transduction histidine kinase involved in
nitrogen fixation and metabolism regulation [Signal
transduction mechanisms].
Length = 712
Score = 28.6 bits (64), Expect = 1.3
Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 43 EPGIEITTMIYSVGYT-LSLIALIIAVWIFVYFKD 76
E G + + +++ Y +L+ L+ A+W + F
Sbjct: 269 EAGRDGLQIAFALLYLSTALLVLLAAIWTAIAFAR 303
>gnl|CDD|113511 pfam04744, Monooxygenase_B, Monooxygenase subunit B protein.
Family of membrane associated monooxygenases (EC
1.13.12.-) which utilise O(2) to oxidise their
substrate. Family members include both ammonia and
methane monooxygenases involved in the oxidation of
their respective substrates. These enzymes are
multi-subunit complexes. This family represents the B
subunit of the enzyme; the A subunit is thought to
contain the active site..
Length = 381
Score = 27.8 bits (62), Expect = 1.7
Identities = 17/62 (27%), Positives = 22/62 (35%), Gaps = 10/62 (16%)
Query: 14 KWCNANGSWNSFANYSLCTDIKKTTQDLSEPGIEITTMIYSVGYTLSLIALIIAV-WIFV 72
KW GS F N T + T DL T G L +I+ + WI
Sbjct: 122 KWITITGSMADFTNP--VTLLTGETVDLE-------TYNIGNGIFWHLFWMILGIAWIGY 172
Query: 73 YF 74
+F
Sbjct: 173 WF 174
>gnl|CDD|211664 TIGR01512, ATPase-IB2_Cd, heavy
metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase.
This model describes the P-type ATPase primarily
responsible for translocating cadmium ions (and other
closely-related divalent heavy metals such as cobalt,
mercury, lead and zinc) across biological membranes.
These transporters are found in prokaryotes and plants.
Experimentally characterized members of the seed
alignment include: SP|P37617 from E. coli, SP|Q10866
from Mycobacterium tuberculosis and SP|Q59998 from
Synechocystis PCC6803. The cadmium P-type ATPases have
been characterized as Type IB based on a phylogenetic
analysis which combines the copper-translocating ATPases
with the cadmium-translocating species. This model and
that describing the copper-ATPases (TIGR01511) are well
separated, and thus we further type the copper-ATPases
as IB1 and the cadmium-ATPases as IB2. Several sequences
which have not been characterized experimentally fall
just below trusted cutoff for both of these models
(SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from
Sulfolobus solfataricus, OMNI|NTL01CJ01098 from
Campylobacter jejuni, OMNI|NTL01HS01687 from
Halobacterium sp., GP|6899169 from Ureaplasma
urealyticum and OMNI|HP1503 from Helicobacter pylori)
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 536
Score = 27.3 bits (61), Expect = 2.8
Identities = 7/43 (16%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 34 IKKTTQDLSEPGIEITTMI--YSVGYTLSLIALIIAVWIFVYF 74
+ + S + I ++ YT ++A+ +A+W+
Sbjct: 148 VNLVEEAQSRKA-KTQRFIDRFARYYTPVVLAIALAIWLVPGL 189
>gnl|CDD|220778 pfam10487, Nup188, Nucleoporin subcomplex protein binding to Pom34.
This is one of the many peptides that make up the
nucleoporin complex (NPC), and is found across
eukaryotes. The Nup188 subcomplex
(Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six
that make up the NPC, and as such is symmetrically
localised on both faces of the NPC at the nuclear end,
being integrally bound to the C-terminus of Pom34p.
Length = 931
Score = 27.2 bits (60), Expect = 3.4
Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 5/50 (10%)
Query: 70 IFVYFKDL-RCLRN-KIHTNLMCTYILADFMWILTMTVQMSVQSNFACVI 117
+F L L +T MC + L I + S N +I
Sbjct: 343 VFQKLTKLSESLSFDTAYTACMCIFGLLSLNLI---PLTASTTGNIQSII 389
>gnl|CDD|173809 cd07483, Peptidases_S8_Subtilisin_Novo-like, Peptidase S8 family
domain in Subtilisin_Novo-like proteins. Subtilisins
are a group of alkaline proteinases originating from
different strains of Bacillus subtilis. Novo is one of
the strains that produced enzymes belonging to this
group. The enzymes obtained from the Novo and BPN'
strains are identical. The Carlsburg and Novo
subtilisins are thought to have arisen from a common
ancestral protein. They have similar peptidase and
esterase activities, pH profiles, catalyze
transesterification reactions, and are both inhibited by
diispropyl fluorophosphate, though they differ in 85
positions in the amino acid sequence. Members of the
peptidases S8 and S35 clan include endopeptidases,
exopeptidases and also a tripeptidyl-peptidase. The S8
family has an Asp/His/Ser catalytic triad similar to
that found in trypsin-like proteases, but do not share
their three-dimensional structure and are not homologous
to trypsin. The S53 family contains a catalytic triad
Glu/Asp/Ser with an additional acidic residue Asp in the
oxyanion hole, similar to that of subtilisin.. The
stability of these enzymes may be enhanced by calcium,
some members have been shown to bind up to 4 ions via
binding sites with different affinity. Some members of
this clan contain disulfide bonds. These enzymes can be
intra- and extracellular, some function at extreme
temperatures and pH values.
Length = 291
Score = 26.6 bits (59), Expect = 5.2
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 13/73 (17%)
Query: 12 ASKWCNANGSWNSFANYSLCTDIKKTTQDLSEPGIEITTMIYSVGYTL----SLIALI-- 65
AS N +F+NY K D+ PG I + Y S+ A +
Sbjct: 211 ASSKKYENNLVANFSNYG------KKNVDVFAPGERIYSTTPDNEYETDSGTSMAAPVVS 264
Query: 66 -IAVWIFVYFKDL 77
+A I+ Y+ +L
Sbjct: 265 GVAALIWSYYPNL 277
>gnl|CDD|180506 PRK06279, PRK06279, putative monovalent cation/H+ antiporter
subunit E; Reviewed.
Length = 100
Score = 25.4 bits (56), Expect = 5.9
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 49 TTMIYSVGYTLSLIALIIAVWIFVYFKDLRCLRNKI 84
++Y +GY + LI II WI V R L KI
Sbjct: 1 MRLLYGIGYLIVLIKAIIEAWIDVVK---RSLNGKI 33
>gnl|CDD|179444 PRK02557, psbE, cytochrome b559 subunit alpha; Provisional.
Length = 81
Score = 24.6 bits (54), Expect = 8.8
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 48 ITTMIYSVGYTLSLIALIIAVWIFVY 73
IT++ Y V + +++ AL IA W+FV
Sbjct: 14 ITSIRYWVIHAITIPALFIAGWLFVS 39
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1). All proteins
in this family with known functions are ATP-dependent
DNA ligases. Functions include DNA repair, DNA
replication, and DNA recombination (or any process
requiring ligation of two single-stranded DNA sections).
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 514
Score = 25.7 bits (57), Expect = 9.6
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 28 YSLCTDIKKTTQDLSEPGIE 47
++L D+ K + L E G+
Sbjct: 134 FNLTNDLGKVAKILLEEGLR 153
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
0.331 0.139 0.465
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,741,537
Number of extensions: 569614
Number of successful extensions: 1136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1124
Number of HSP's successfully gapped: 81
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 54 (24.6 bits)