RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9139
(197 letters)
>gnl|CDD|238020 cd00063, FN3, Fibronectin type 3 domain; One of three types of
internal repeats found in the plasma protein
fibronectin. Its tenth fibronectin type III repeat
contains an RGD cell recognition sequence in a flexible
loop between 2 strands. Approximately 2% of all animal
proteins contain the FN3 repeat; including extracellular
and intracellular proteins, membrane spanning cytokine
receptors, growth hormone receptors, tyrosine
phosphatase receptors, and adhesion molecules. FN3-like
domains are also found in bacterial glycosyl hydrolases.
Length = 93
Score = 67.9 bits (166), Expect = 2e-15
Identities = 34/93 (36%), Positives = 53/93 (56%), Gaps = 2/93 (2%)
Query: 27 PPGVPNILLQSTTTHSISILWKPSYDGGAIITHYIVSYRDR-TEDWQSVHVDAEYR-EFT 84
P N+ + T+ S+++ W P D G IT Y+V YR++ + DW+ V V +T
Sbjct: 1 PSPPTNLRVTDVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSGDWKEVEVTPGSETSYT 60
Query: 85 LTQLKCGTHYKINIKLVNSIGESKPSKTIAAST 117
LT LK GT Y+ ++ VN GES PS+++ +T
Sbjct: 61 LTGLKPGTEYEFRVRAVNGGGESPPSESVTVTT 93
>gnl|CDD|214495 smart00060, FN3, Fibronectin type 3 domain. One of three types of
internal repeat within the plasma protein, fibronectin.
The tenth fibronectin type III repeat contains a RGD
cell recognition sequence in a flexible loop between 2
strands. Type III modules are present in both
extracellular and intracellular proteins.
Length = 83
Score = 63.8 bits (155), Expect = 7e-14
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 27 PPGVPNILLQSTTTHSISILWKPSYDGGAI--ITHYIVSYRDRTEDWQSVHVDAEYREFT 84
P N+ + T+ S+++ W+P D G I Y V YR+ +W+ V+V +T
Sbjct: 1 PSPPSNLRVTDVTSTSVTLSWEPPPDDGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYT 60
Query: 85 LTQLKCGTHYKINIKLVNSIGES 107
LT LK GT Y+ ++ VN GE
Sbjct: 61 LTGLKPGTEYEFRVRAVNGAGEG 83
>gnl|CDD|200951 pfam00041, fn3, Fibronectin type III domain.
Length = 84
Score = 57.8 bits (140), Expect = 1e-11
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 26 SPPGVPNILLQSTTTHSISILWKPSYDGGAIITHYIVSYR--DRTEDWQSVHVDAEYREF 83
S P N+ + T+ S+++ W P G I T Y V YR + E+W+ + V +
Sbjct: 1 SAPT--NLTVTDVTSTSLTLSWSPPPGNGPI-TGYEVEYRPVNGGEEWKEITVPGTTTSY 57
Query: 84 TLTQLKCGTHYKINIKLVNSIGESKPS 110
TLT LK GT Y++ ++ VN GE PS
Sbjct: 58 TLTGLKPGTEYEVRVQAVNGAGEGPPS 84
>gnl|CDD|224959 COG2048, HdrB, Heterodisulfide reductase, subunit B [Energy
production and conversion].
Length = 293
Score = 29.6 bits (67), Expect = 0.85
Identities = 13/46 (28%), Positives = 15/46 (32%), Gaps = 6/46 (13%)
Query: 51 YDGGAIITHYI-VSYRDRTEDWQSVHVDAEYREFTLTQLKCGTHYK 95
Y G + H Y D V E + LT LK HY
Sbjct: 113 YKGSTHVNHVAEALYNDL-----GVEKIKEKVKKPLTGLKVAVHYG 153
>gnl|CDD|184980 PRK15019, PRK15019, CsdA-binding activator; Provisional.
Length = 147
Score = 28.8 bits (64), Expect = 1.1
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 126 INIPLSNLDEALEMPLVIENLLPATRYELTISAKNDAGSTNKNYVFATLSVNGGKAF 182
PL+ ++ +++ LPA EL AK AG N+ ++ T++ NG F
Sbjct: 23 TFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHF 79
>gnl|CDD|143227 cd05750, Ig_Pro_neuregulin, Immunoglobulin (Ig)-like domain in
neuregulins (NRGs). Ig_Pro_neuregulin: immunoglobulin
(Ig)-like domain in neuregulins (NRGs). NRGs are
signaling molecules, which participate in cell-cell
interactions in the nervous system, breast, heart, and
other organ systems, and are implicated in the
pathology of diseases including schizophrenia, multiple
sclerosis, and breast cancer. There are four members of
the neuregulin gene family (NRG1, -2, -3, and -4). The
NRG-1 protein, binds to and activates the tyrosine
kinases receptors ErbB3 and ErbB4, initiating signaling
cascades. The other NRGs proteins bind one or the other
or both of these ErbBs. NRG-1 has multiple functions;
for example, in the brain it regulates various
processes such as radial glia formation and neuronal
migration, dendritic development, and expression of
neurotransmitters receptors; in the peripheral nervous
system NRG-1 regulates processes such as target cell
differentiation, and Schwann cell survival. There are
many NRG-1 isoforms, which arise from the alternative
splicing of mRNA. Less is known of the functions of the
other NRGs. NRG-2 and -3 are expressed predominantly in
the nervous system. NRG-2 is expressed by motor neurons
and terminal Schwann cells, and is concentrated near
synaptic sites and may be a signal that regulates
synaptic differentiation. NRG-4 has been shown to
direct pancreatic islet cell development towards the
delta-cell lineage.
Length = 75
Score = 27.5 bits (61), Expect = 1.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 3 GNYTCLADNIFGKD 16
G YTC+ +NI G D
Sbjct: 56 GEYTCVVENILGND 69
>gnl|CDD|216580 pfam01575, MaoC_dehydratas, MaoC like domain. The maoC gene is
part of a operon with maoA which is involved in the
synthesis of monoamine oxidase. The MaoC protein is
found to share similarity with a wide variety of
enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal
hydratase-dehydrogenase-epimerase, fatty acid synthase
beta subunit. Several bacterial proteins that are
composed solely of this domain have (R)-specific
enoyl-CoA hydratase activity. This domain is also
present in the NodN nodulation protein N.
Length = 123
Score = 27.7 bits (62), Expect = 2.5
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 61 IVSYRDRTEDWQSVHVDAEY 80
I + + D +HVD E+
Sbjct: 23 IALFALVSGDHNPIHVDPEF 42
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 27.5 bits (62), Expect = 3.3
Identities = 6/22 (27%), Positives = 9/22 (40%), Gaps = 3/22 (13%)
Query: 91 GTHYKINIK---LVNSIGESKP 109
G Y+ + L +G S P
Sbjct: 91 GVGYRAQVVGGNLELFLGYSHP 112
>gnl|CDD|193486 cd04081, CBM35_galactosidase-like, Carbohydrate Binding Module
family 35 (CBM35); appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. This family
includes carbohydrate binding module family 35 (CBM35);
these are non-catalytic carbohydrate binding domains
that are appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. Examples of
proteins which contain CBM35s belonging to this family
includes the CBM35 of an exo-beta-1,3-galactanase from
Phanerochaete chrysosporium 9(Pc1,3Gal43A) which is
appended to a GH43 domain, and the CBM6 of domain of
two bifunctional proteins with
beta-L-arabinopyranosidase/alpha-D-galactopyranosidase
activities from Fusarium oxysporum 12S, Foap1 and Foap2
(Fo/AP1 and Fo/AP2), that are appended to GH31 domains.
CBM35s are unique in that they display conserved
specificity through extensive sequence similarity but
divergent function through their appended catalytic
modules. They are known to bind alpha-D-galactose (Gal),
mannan (Man), xylan, glucuronic acid (GlcA), a
beta-polymer of mannose, and possibly glucans, forming
four subfamilies based on general ligand specificities
(galacto, urono, manno, and gluco configurations). Some
CBM35s bind their ligands in a calcium-dependent manner.
In contrast to most CBMs that are generally rigid
proteins, CBM35 undergoes significant conformational
change upon ligand binding. GH43 includes
beta-xylosidases and beta-xylanases, using
aryl-glycosides as substrates, while family GH31
includes alpha-glucosidases and alpha-xylosidases that
cleave a terminal carbohydrate moiety from substrates
that vary considerably in size, mostly accommodating
alpha-D-glucose and alpha-D-xylose.
Length = 123
Score = 27.2 bits (61), Expect = 3.4
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 149 ATRYELTISAKNDAGSTNKNYVFATLSVNGGKAF---------HSWSPIQVHTTLN 195
A Y LTI N + +++ T+SVNGG +W V L
Sbjct: 48 AGTYTLTIDYIN-GDTADRS---LTVSVNGGAPTRVAFPGTGGWTWGTSTVPVDLK 99
>gnl|CDD|143202 cd05725, Ig3_Robo, Third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Ig3_Robo: domain similar to
the third immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Robo receptors play a role in
the development of the central nervous system (CNS),
and are receptors of Slit protein. Slit is a repellant
secreted by the neural cells in the midline. Slit acts
through Robo to prevent most neurons from crossing the
midline from either side. Three mammalian Robo homologs
(robo1, -2, and -3), and three mammalian Slit homologs
(Slit-1,-2, -3), have been identified. Commissural
axons, which cross the midline, express low levels of
Robo; longitudinal axons, which avoid the midline,
express high levels of Robo. robo1, -2, and -3 are
expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 69
Score = 26.2 bits (58), Expect = 3.9
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 3 GNYTCLADNIFGK 15
G+YTC A+N+ GK
Sbjct: 48 GSYTCEAENMVGK 60
>gnl|CDD|143170 cd04969, Ig5_Contactin_like, Fifth Ig domain of contactin.
Ig5_Contactin_like: Fifth 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
act ivity 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 = 73
Score = 25.9 bits (57), Expect = 4.2
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 3 GNYTCLADNIFGK 15
G YTC A+N FGK
Sbjct: 52 GKYTCFAENFFGK 64
>gnl|CDD|239525 cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA
hydratase]. Catalyzes the hydration of trans-2-enoyl
CoA to (R)-3-hydroxyacyl-CoA as part of the PHA
(polyhydroxyalkanoate) biosynthetic pathway. The
structure of the monomer includes a five-strand
antiparallel beta-sheet wrapped around a central alpha
helix, referred to as a hot dog fold. The active site
lies within a substrate-binding tunnel formed by the
homodimer. Other enzymes with this fold include MaoC
dehydratase, Hydratase-Dehydrogenase-Epimerase protein
(HDE), and the fatty acid synthase beta subunit.
Length = 127
Score = 26.8 bits (60), Expect = 5.1
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 61 IVSYRDRTEDWQSVHVDAEY 80
I + + D +HVD EY
Sbjct: 15 IALFARLSGDPNPIHVDPEY 34
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 27.2 bits (61), Expect = 6.7
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 23/58 (39%)
Query: 125 WINIPLSNLDEALEMPLVIENLLPATRYELTISAKNDAGSTNKNYVFATLSVNGGKAF 182
W+ +PL+ + + + P RY L LSV GG F
Sbjct: 139 WVRVPLTEIHQ--------GDFSPLFRYTL---------------AIGLLSVAGGWLF 173
>gnl|CDD|143212 cd05735, Ig8_DSCAM, Eight immunoglobulin (Ig) domain of Down
Syndrome Cell Adhesion molecule (DSCAM). Ig8_DSCAM:
the eight immunoglobulin (Ig) domain of Down Syndrome
Cell Adhesion molecule (DSCAM). DSCAM is a cell
adhesion molecule expressed largely in the developing
nervous system. The gene encoding DSCAM is located at
human chromosome 21q22, the locus associated with the
mental retardation phenotype of Down Syndrome. DSCAM is
predicted to be the largest member of the IG
superfamily. It has been demonstrated that DSCAM can
mediate cation-independent homophilic intercellular
adhesion.
Length = 88
Score = 25.8 bits (56), Expect = 6.7
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 3 GNYTCLADNIFGKDDIYYQVTILSPPGVP 31
G ++C A N +G+D Q+T+ PP P
Sbjct: 60 GFFSCHAINSYGEDRGIIQLTVQEPPDPP 88
>gnl|CDD|239534 cd03450, NodN, NodN (nodulation factor N) contains a single hot
dog fold similar to those of the peroxisomal
Hydratase-Dehydrogenase-Epimerase (HDE) protein, and
the fatty acid synthase beta subunit. Rhizobium and
related species form nodules on the roots of their
legume hosts, a symbiotic process that requires
production of Nod factors, which are signal molecules
involved in root hair deformation and meristematic cell
division. The nodulation gene products, including
NodN, are involved in producing the Nod factors,
however the role played by NodN is unclear.
Length = 149
Score = 26.4 bits (59), Expect = 6.9
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 66 DRTEDWQSVHVDAE 79
D T D Q +HVD E
Sbjct: 34 DATGDHQWIHVDPE 47
>gnl|CDD|180518 PRK06294, PRK06294, coproporphyrinogen III oxidase; Provisional.
Length = 370
Score = 27.0 bits (60), Expect = 7.3
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 130 LSNLDEALEMPLVIENLLPA---TRYELTISAKNDAGSTNKNY 169
+++ + EM L E LL + TRYEL AK A S + Y
Sbjct: 211 IADEEILAEMSLAAEELLTSQGFTRYELASYAKPQAQSKHNTY 253
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
0.315 0.132 0.393
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,701,026
Number of extensions: 855636
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 653
Number of HSP's successfully gapped: 28
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.7 bits)