RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5697
(145 letters)
>gnl|CDD|143210 cd05733, Ig6_L1-CAM_like, Sixth immunoglobulin (Ig)-like domain of
the L1 cell adhesion molecule (CAM) and similar
proteins. Ig6_L1-CAM_like: domain similar to the sixth
immunoglobulin (Ig)-like domain of the L1 cell adhesion
molecule (CAM). L1 belongs to the L1 subfamily of cell
adhesion molecules (CAMs) and is comprised of an
extracellular region having six Ig-like domains and five
fibronectin type III domains, a transmembrane region and
an intracellular domain. L1 is primarily expressed in
the nervous system and is involved in its development
and function. L1 is associated with an X-linked
recessive disorder, X-linked hydrocephalus, MASA
syndrome, or spastic paraplegia type 1, that involves
abnormalities of axonal growth. This group also contains
NrCAM [Ng(neuronglia)CAM-related cell adhesion
molecule], which is primarily expressed in the nervous
system, and human neurofascin.
Length = 77
Score = 32.0 bits (73), Expect = 0.025
Identities = 15/49 (30%), Positives = 23/49 (46%)
Query: 89 KDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSRFVHV 137
KD R+ + S G R + + Y+C ASNE G +S +H+
Sbjct: 28 KDPRVTMKPDSGTLVIDNMNGGRAEDYEGEYQCYASNELGTAISNEIHL 76
>gnl|CDD|143275 cd05867, Ig4_L1-CAM_like, Fourth immunoglobulin (Ig)-like domain of
the L1 cell adhesion molecule (CAM). Ig4_L1-CAM_like:
fourth immunoglobulin (Ig)-like domain of the L1 cell
adhesion molecule (CAM). L1 is comprised of an
extracellular region having six Ig-like domains and five
fibronectin type III domains, a transmembrane region and
an intracellular domain. L1 is primarily expressed in
the nervous system and is involved in its development
and function. L1 is associated with an X-linked
recessive disorder, X-linked hydrocephalus, MASA
syndrome, or spastic paraplegia type 1, that involves
abnormalities of axonal growth. This group also contains
the chicken neuron-glia cell adhesion molecule, Ng-CAM.
Length = 76
Score = 30.2 bits (68), Expect = 0.080
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 74 QLGWRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSR 133
+ W + + D R +S+G+L+ +P + VY+C A N G +L+
Sbjct: 17 NITWSINGAPIEGTDPDPRRHVSSGALILT-----DVQPS-DTAVYQCEARNRHGNLLAN 70
Query: 134 -FVHV 137
VHV
Sbjct: 71 AHVHV 75
>gnl|CDD|143179 cd04978, Ig4_L1-NrCAM_like, Fourth immunoglobulin (Ig)-like domain
of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule),
and NrCAM (Ng-CAM-related). Ig4_L1-NrCAM_like: fourth
immunoglobulin (Ig)-like domain of L1, Ng-CAM
(Neuron-glia CAM cell adhesion molecule), and NrCAM
(Ng-CAM-related). These proteins belong to the L1
subfamily of cell adhesion molecules (CAMs) and are
comprised of an extracellular region having six Ig-like
domains and five fibronectin type III domains, a
transmembrane region and an intracellular domain. These
molecules are primarily expressed in the nervous system.
L1 is associated with an X-linked recessive disorder,
X-linked hydrocephalus, MASA syndrome, or spastic
paraplegia type 1, that involves abnormalities of axonal
growth.
Length = 76
Score = 30.1 bits (68), Expect = 0.12
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 7/62 (11%)
Query: 77 WRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSR-FV 135
WR + + D R + G+L+ + VY+C ASN G +L+ FV
Sbjct: 20 WRLNGVPIEELPPDPRRRVDGGTLILSNVQPN------DTAVYQCNASNVHGYLLANAFV 73
Query: 136 HV 137
HV
Sbjct: 74 HV 75
>gnl|CDD|206066 pfam13895, Ig_2, Immunoglobulin domain. This domain contains
immunoglobulin-like domains.
Length = 80
Score = 29.7 bits (67), Expect = 0.14
Identities = 12/40 (30%), Positives = 14/40 (35%), Gaps = 3/40 (7%)
Query: 102 FPPFPETGFRPDV---HSTVYRCRASNEAGVILSRFVHVK 138
F P+V S Y C ASN G S V +
Sbjct: 40 LSSSQNGFFTPNVSAEDSGTYTCVASNGGGGKTSNPVTLT 79
>gnl|CDD|143256 cd05848, Ig1_Contactin-5, First Ig domain of contactin-5.
Ig1_Contactin-5: First Ig domain of the neural cell
adhesion molecule contactin-5. Contactins are comprised
of six Ig domains followed by four fibronectin type III
(FnIII) domains, anchored to the membrane by
glycosylphosphatidylinositol. The different contactins
show different expression patterns in the central
nervous system. In rats, a lack of contactin-5 (NB-2)
results in an impairment of the neuronal activity in the
auditory system. Contactin-5 is expressed specifically
in the postnatal nervous system, peaking at about 3
weeks postnatal. Contactin-5 is highly expressed in the
adult human brain in the occipital lobe and in the
amygdala; lower levels of expression have been detected
in the corpus callosum, caudate nucleus, and spinal
cord.
Length = 94
Score = 29.1 bits (65), Expect = 0.27
Identities = 19/53 (35%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 81 NNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSR 133
N T I D R +L +G+L+ E S Y+C A+N G ILSR
Sbjct: 41 NGTEIDTESDYRYSLIDGNLIISNPSEV-----KDSGRYQCLATNSIGSILSR 88
>gnl|CDD|143199 cd05722, Ig1_Neogenin, First immunoglobulin (Ig)-like domain in
neogenin and similar proteins. Ig1_Neogenin: first
immunoglobulin (Ig)-like domain in neogenin and related
proteins. Neogenin is a cell surface protein which is
expressed in the developing nervous system of vertebrate
embryos in the growing nerve cells. It is also expressed
in other embryonic tissues, and may play a general role
in developmental processes such as cell migration,
cell-cell recognition, and tissue growth regulation.
Included in this group is the tumor suppressor protein
DCC, which is deleted in colorectal carcinoma . DCC and
neogenin each have four Ig-like domains followed by six
fibronectin type III domains, a transmembrane domain,
and an intracellular domain.
Length = 95
Score = 29.0 bits (65), Expect = 0.32
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 72 PSQLGWRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGF-RPDVHSTVYRCRASNEA-GV 129
P ++ W+ + + R L NGSL+ + +PD Y+C A N++ G
Sbjct: 28 PPKIEWKKDGVLLNLVSDERRQQLPNGSLLITSVVHSKHNKPD--EGFYQCVAQNDSLGS 85
Query: 130 ILSR 133
I+SR
Sbjct: 86 IVSR 89
>gnl|CDD|143282 cd05874, Ig6_NrCAM, Sixth immunoglobulin (Ig)-like domain of NrCAM
(Ng (neuronglia) CAM-related cell adhesion molecule).
Ig6_NrCAM: sixth immunoglobulin (Ig)-like domain of
NrCAM (Ng (neuronglia) CAM-related cell adhesion
molecule). NrCAM belongs to the L1 subfamily of cell
adhesion molecules (CAMs) and is comprised of an
extracellular region having six Ig-like domains and five
fibronectin type III domains, a transmembrane region,
and an intracellular domain. NrCAM is primarily
expressed in the nervous system.
Length = 77
Score = 27.2 bits (60), Expect = 1.2
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 109 GFRPDVHSTVYRCRASNEAGVILSRFVHVK 138
G + + + VY+C A NE G +S + ++
Sbjct: 48 GEKAEAYEGVYQCTARNERGAAVSNNIVIR 77
>gnl|CDD|143168 cd04967, Ig1_Contactin, First Ig domain of contactin.
Ig1_Contactin: First Ig domain of contactins. Contactins
are neural cell adhesion molecules and are comprised of
six Ig domains followed by four fibronectin type
III(FnIII) domains anchored to the membrane by
glycosylphosphatidylinositol. The first four Ig domains
form the intermolecular binding fragment, which arranges
as a compact U-shaped module via contacts between Ig
domains 1 and 4, and between Ig domains 2 and 3.
Contactin-2 (TAG-1, axonin-1) may play a part in the
neuronal processes of neurite outgrowth, axon guidance
and fasciculation, and neuronal migration. This group
also includes contactin-1 and contactin-5. The different
contactins show different expression patterns in the
central nervous system. During development and in
adulthood, contactin-2 is transiently expressed in
subsets of central and peripheral neurons. Contactin-5
is expressed specifically in the rat postnatal nervous
system, peaking at about 3 weeks postnatal, and a lack
of contactin-5 (NB-2) results in an impairment of
neuronal activity in the rat auditory system.
Contactin-5 is highly expressed in the adult human brain
in the occipital lobe and in the amygdala. Contactin-1
is differentially expressed in tumor tissues and may,
through a RhoA mechanism, facilitate invasion and
metastasis of human lung adenocarcinoma.
Length = 91
Score = 27.4 bits (61), Expect = 1.4
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 77 WRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSR 133
W N T I D R +L G+L+ P + Y+C ASN G +LSR
Sbjct: 38 WLM-NGTEIDDEPDSRYSLVGGNLVISN-PSKA----KDAGRYQCLASNIVGTVLSR 88
>gnl|CDD|218998 pfam06356, DUF1064, Protein of unknown function (DUF1064). This
family consists of several phage and bacterial proteins
of unknown function.
Length = 118
Score = 26.8 bits (59), Expect = 2.9
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 10/69 (14%)
Query: 34 NIVYSSRSENEHYPFRIKSAPGGNRTRGLELTRQTRYEPSQLGWRFSNNTV----IAYVK 89
IV+ S++E E+Y + GGN R + Q ++E L +F N I Y
Sbjct: 13 GIVFDSKAECEYYQQLKSNMNGGNYDR---IELQPKFE---LQPKFRKNGKLYRAIRYKA 66
Query: 90 DLRIALSNG 98
D + S G
Sbjct: 67 DFTLRNSAG 75
>gnl|CDD|143276 cd05868, Ig4_NrCAM, Fourth immunoglobulin (Ig)-like domain of NrCAM
(NgCAM-related cell adhesion molecule). Ig4_ NrCAM:
fourth immunoglobulin (Ig)-like domain of NrCAM
(NgCAM-related cell adhesion molecule). NrCAM belongs to
the L1 subfamily of cell adhesion molecules (CAMs) and
is comprised of an extracellular region having six
IG-like domains and five fibronectin type III domains, a
transmembrane region and an intracellular domain. NrCAM
is primarily expressed in the nervous system.
Length = 76
Score = 26.1 bits (57), Expect = 3.1
Identities = 13/23 (56%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 116 STVYRCRASNEAGVILSR-FVHV 137
S VY+C ASNE G +L+ FV+V
Sbjct: 53 SAVYQCNASNEYGYLLANAFVNV 75
>gnl|CDD|143165 cd00096, Ig, Immunoglobulin domain. Ig: immunoglobulin (Ig) domain
found in the Ig superfamily. The Ig superfamily is a
heterogenous group of proteins, built on a common fold
comprised of a sandwich of two beta sheets. Members of
this group are components of immunoglobulin, neuroglia,
cell surface glycoproteins, such as, T-cell receptors,
CD2, CD4, CD8, and membrane glycoproteins, such as,
butyrophilin and chondroitin sulfate proteoglycan core
protein. A predominant feature of most Ig domains is a
disulfide bridge connecting the two beta-sheets with a
tryptophan residue packed against the disulfide bond.
Length = 74
Score = 25.5 bits (55), Expect = 5.2
Identities = 9/51 (17%), Positives = 16/51 (31%), Gaps = 6/51 (11%)
Query: 80 SNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVI 130
++ + + + +L S Y C ASN AG +
Sbjct: 25 PSSVLTRVRSSRGTSSGSSTLTISNVTLE------DSGTYTCVASNSAGTV 69
>gnl|CDD|143283 cd05875, Ig6_hNeurofascin_like, Sixth immunoglobulin (Ig)-like
domain of human neurofascin (NF).
Ig6_hNeurofascin_like: the sixth immunoglobulin
(Ig)-like domain of human neurofascin (NF). NF belongs
to the L1 subfamily of cell adhesion molecules (CAMs)
and is comprised of an extracellular region having six
Ig-like domains and five fibronectin type III domains, a
transmembrane region, and a cytoplasmic domain. NF has
many alternatively spliced isoforms having different
temporal expression patterns during development. NF
participates in axon subcellular targeting and synapse
formation, however little is known of the functions of
the different isoforms.
Length = 77
Score = 25.3 bits (55), Expect = 6.2
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 77 WRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVYRCRASNEAGVILSRFVH 136
W N KD R+++ S G RP+ + Y+C A N G LS +
Sbjct: 17 WT-RNGKFFNVAKDPRVSMRRRSGTLVIDFSGGGRPEDYEGEYQCFARNNLGTALSNKIL 75
Query: 137 VK 138
++
Sbjct: 76 LQ 77
>gnl|CDD|238675 cd01379, MYSc_type_III, Myosin motor domain, type III myosins.
Myosin III has been shown to play a role in the vision
process in insects and in hearing in mammals. Myosin
III, an unconventional myosin, does not form dimers.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 653
Score = 26.7 bits (59), Expect = 6.2
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 74 QLGWRFSNNTVIAYVKDLRIALSNGSLMFPPFPETGFRPDVHSTVY 119
QL R+ N + YV D+ IA++ PF + G HS +Y
Sbjct: 19 QLQKRYETNQIYTYVGDILIAVN-------PFQQLGLYTTQHSRLY 57
>gnl|CDD|180433 PRK06157, PRK06157, acetyl-CoA acetyltransferase; Validated.
Length = 398
Score = 26.5 bits (59), Expect = 6.7
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 85 IAYVKDLRIALSNGS-LMFPPFPETGFRPDVHSTVYRC-RASNEAGV 129
YVK L++A+SNG L + + + F +T +A EAG+
Sbjct: 239 PVYVKALQLAVSNGWELQYNGWDGSYF----PTTRIAARKAYREAGI 281
>gnl|CDD|220261 pfam09484, Cas_TM1802, CRISPR-associated protein TM1802
(cas_TM1802). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This minor cas protein is
found in at least five prokaryotic genomes:
Methanosarcina mazei, Sulfurihydrogenibium azorense,
Thermotoga maritima, Carboxydothermus hydrogenoformans,
and Dictyoglomus thermophilum, the first of which is
archaeal while the rest are bacterial.
Length = 584
Score = 26.2 bits (58), Expect = 7.1
Identities = 13/49 (26%), Positives = 16/49 (32%), Gaps = 7/49 (14%)
Query: 7 STLLADADTYIIADRSLFPRP-------LGYLVGNIVYSSRSENEHYPF 48
L D D + F P LG LVG I+ + PF
Sbjct: 464 LDLDEDIDEFFSKYEEFFNSPQKKALFLLGVLVGKILNKQYKKRGSKPF 512
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 25.3 bits (56), Expect = 7.2
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 118 VYRCRASNEAG 128
Y C A+N AG
Sbjct: 70 KYTCVATNSAG 80
>gnl|CDD|238590 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases, N-
and C-terminal domains. This CD includes various
bacterial integrases, including cLV25, a Bacteroides
fragilis chromosomal transfer factor integrase similar
to the Bacteroides mobilizable transposon, Tn4399,
integrase.
Length = 299
Score = 25.7 bits (57), Expect = 9.6
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 80 SNNTVIAYVKDLR----IALSNGSLMFPPFPETGFRPD 113
S NT + Y+ L+ IA + L PF + + +
Sbjct: 85 SRNTAVHYLSWLKKLLKIAYRDKGLRDNPFAKFKCKKE 122
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
0.322 0.138 0.417
Gapped
Lambda K H
0.267 0.0667 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,327,519
Number of extensions: 636253
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 452
Number of HSP's successfully gapped: 28
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.9 bits)
S2: 54 (24.7 bits)