RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12771
(160 letters)
>gnl|CDD|200499 cd11238, Sema_2A, The Sema domain, a protein interacting module, of
semaphorin 2A (Sema2A). Sema2A, a secreted semaphorin,
signals through its receptor plexin B (PlexB) to
regulate central and peripheral axon pathfinding. In the
Drosophila embryo, Sema2A secreted by oenocytes
interacts with PlexB to guide sensory axons. Sema2A is a
member of the semaphorin family of proteins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 452
Score = 153 bits (389), Expect = 2e-45
Identities = 63/93 (67%), Positives = 75/93 (80%), Gaps = 3/93 (3%)
Query: 57 ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
+L+ NL HL E+VPG G+GI KCPYDP+DNSTA+WVE GNPG+LPALYSGT EFTKA
Sbjct: 94 VLDANLLHLP--EYVPGPGNGIGKCPYDPDDNSTAVWVEWGNPGDLPALYSGTRTEFTKA 151
Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
+TVI+R L N T G+ E +F RT+KYDSKWLD
Sbjct: 152 NTVIYRPPLYNNTKGRHE-SFMRTLKYDSKWLD 183
>gnl|CDD|200496 cd11235, Sema_semaphorin, The Sema domain, a protein interacting
module, of semaphorins. Semaphorins are regulator
molecules in the development of the nervous system and
in axonal guidance. They also play important roles in
other biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. They can be
divided into 7 classes. Vertebrates have members in
classes 3-7, whereas classes 1 and 2 are known only in
invertebrates. Class 2 and 3 semaphorins are secreted
proteins; classes 1 and 4 through 6 are transmembrane
proteins; and class 7 is membrane associated via
glycosylphosphatidylinositol (GPI) linkage. The
semaphorins exert their function through their
receptors, the neuropilin and plexin families. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 437
Score = 84.0 bits (208), Expect = 1e-19
Identities = 34/85 (40%), Positives = 44/85 (51%), Gaps = 15/85 (17%)
Query: 65 LGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTD 124
+ E V SG KCPYDP+ NSTA++ + LYSGT+A+F D VI+RT
Sbjct: 91 VETFELVGKEESGRGKCPYDPDHNSTALFADGE-------LYSGTSADFLGTDPVIYRTL 143
Query: 125 LLNFTTGKKEYTFKRTIKYDSKWLD 149
N RT +DSKWL+
Sbjct: 144 GHN--------PPLRTEYHDSKWLN 160
>gnl|CDD|200526 cd11265, Sema_5C, The Sema domain, a protein interacting module, of
semaphorin 5C (sema5C). In Drosophila, Sema5C was
identified as an early development gene, which is
expressed in stage 2 embryos with a striped pattern
emerging at later stages. Sema5c may play a role in
odor-guided behavior and in tumorigenesis. Sema5C
belongs to class 5 semaphorin family of proteins, which
are transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 433
Score = 59.8 bits (145), Expect = 4e-11
Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 12/79 (15%)
Query: 71 VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTT 130
V SG+AKCPY P+ N TA+ G L+ G+ +F+ +D+ I+RT
Sbjct: 102 VTEWDSGVAKCPYSPHANITALLSSSGQ------LFVGSPTDFSGSDSAIYRTL------ 149
Query: 131 GKKEYTFKRTIKYDSKWLD 149
G +F RT +Y+SKWL+
Sbjct: 150 GTSNKSFLRTKQYNSKWLN 168
>gnl|CDD|216480 pfam01403, Sema, Sema domain. The Sema domain occurs in
semaphorins, which are a large family of secreted and
transmembrane proteins, some of which function as
repellent signals during axon guidance. Sema domains
also occur in the hepatocyte growth factor receptor and
human plexin A-3.
Length = 435
Score = 58.5 bits (142), Expect = 8e-11
Identities = 28/89 (31%), Positives = 34/89 (38%), Gaps = 15/89 (16%)
Query: 60 NNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTV 119
N V G CPYDP NST++ + G LYSGT +F+ D
Sbjct: 91 NLGDRCLFSLDVDKEEDGCGDCPYDPLGNSTSV-LVDGE------LYSGTVIDFSGRDPS 143
Query: 120 IFRTDLLNFTTGKKEYTFKRTIKYDSKWL 148
I R Y RT +DSK L
Sbjct: 144 IRRL--------LGSYDGLRTEFHDSKLL 164
>gnl|CDD|200498 cd11237, Sema_1A, The Sema domain, a protein interacting module, of
semaphorin 1A (Sema1A). Sema1A is a transmembrane
protein. It has been shown to mediate the
defasciculation of motor axon bundles at specific choice
points. Sema1A binds to its receptor plexin A (PlexA),
which in turn triggers downstream signaling events
involving the receptor tyrosine kinase Otk, the
evolutionarily conserved flavoprotein monooxygenase
molecule interacting with CasL (MICAL), and the A kinase
anchoring protein Nervy, leading to repulsive
growth-cone response. Sema1A has also been shown to be
involved in synaptic formation. It is a member of the
semaphorin family of proteins. Semaphorins are
regulatory molecules in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 446
Score = 55.4 bits (134), Expect = 1e-09
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 20/75 (26%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
G CPYDP NSTA++ + G LYS T A+F+ AD +I+R L
Sbjct: 105 DGQGLCPYDPKHNSTAVYAD-GQ------LYSATVADFSGADPLIYREPL---------- 147
Query: 136 TFKRTIKYDSKWLDS 150
RT +YD K L++
Sbjct: 148 ---RTERYDLKQLNA 159
>gnl|CDD|200525 cd11264, Sema_5B, The Sema domain, a protein interacting module, of
semaphorin 5B (Sema5B). Sema5B is expressed in regions
of the basal telencephalon in rat. Sema5B is an
inhibitory cue for corticofugal axons and acts as a
source of repulsion for the appropriate guidance of
cortical axons away from structures such as the
ventricular zone as they navigate toward and within
subcortical regions. In addition to its role as a
guidance cue, Sema5B regulates the development and
maintenance of synapse size and number in hippocampal
neurons. In addition, the sema domain of Sema5B can be
cleaved of the whole protein and exerts its function in
regulation of synapse morphology. Sema5B belongs to the
class 5 semaphorin family of proteins, which are
transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 437
Score = 52.3 bits (125), Expect = 1e-08
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 14/74 (18%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
+G+A+CPYDP NSTA+ +G LY+ T +F+ D I+R+ L +
Sbjct: 107 NGVARCPYDPRHNSTAVITSRGE------LYAATVIDFSGRDPAIYRS-LGSVPP----- 154
Query: 136 TFKRTIKYDSKWLD 149
RT +Y+SKWL+
Sbjct: 155 --LRTAQYNSKWLN 166
>gnl|CDD|200503 cd11242, Sema_6, The Sema domain, a protein interacting module, of
class 6 semaphorins (Sema6). Class 6 semaphorins
(Sema6s) are membrane associated semaphorins. There are
6 subfamilies named 6A to 6D. Sema6s bind to plexin As
in a neuropilin independent fashion. Sema6-plexin A
signaling plays important roles in lamina-specific axon
projections. Interactions between plexin A2, plexin A4,
and Sema6A control lamina-restricted projection of
hippocampal mossy fibers. Interactions between Sema6C,
Sema6D and plexin A1 shape the stereotypic trajectories
of sensory axons in the spinal cord. In addition to axon
targeting, Sema6D-plexin A1 interactions influence a
wide range of other biological processes. During cardiac
development, Sema6D attracts or repels endothelial cells
in the cardiac tube depending on the expression patterns
of specific coreceptors in addition to plexin A1.
Furthermore, Sema6D binds a receptor complex comprising
of plexin A1, Trem2 (triggering receptor expressed on
myeloid cells 2), and DAP12 on dendritic cells and
osteoclasts to mediate T-cell-DC interactions and to
control bone development, respectively. The Sema domain
is located at the N-terminus and contains four disulfide
bonds formed by eight conserved cysteine residues. It
serves as a receptor-recognition and -binding module.
Length = 465
Score = 51.4 bits (123), Expect = 3e-08
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CP+D + A++ + LYS T +F +D VI+R+ +
Sbjct: 113 SGMARCPFDAKQANVALFADG-------KLYSATVTDFLASDAVIYRS--------LGDS 157
Query: 136 TFKRTIKYDSKWL 148
RT+KYDSKWL
Sbjct: 158 PTLRTVKYDSKWL 170
>gnl|CDD|200500 cd11239, Sema_3, The Sema domain, a protein interacting module, of
class 3 semaphorins. Class 3 semaphorins (Sema3s) are
secreted regulator molecules involved in the development
of the nervous system, vasculogenesis, angiogenesis,and
tumorigenesis. There are 7 distinct subfamilies named
Sema3A to 3G. Sema3s function as repellent signals
during axon guidance by repelling neurons away from the
source of Sema3s. However, Sema3s that are secreted by
tumor cells play an inhibitory role in tumor growth and
angiogenesis (specifically Sema3B and Sema3F). Sema3s
functions by forming complexes with neuropilins and
A-type plexins, where neuropilins serve as the ligand
binding moiety and the plexins function as signal
transduction component. Sema3s primarily inhibit the
cell motility and migration of tumor and endothelial
cells by inducing collapse of the actin cytoskeleton via
neuropilins and plexins. The Sema domain is located at
the N-terminus and contains four disulfide bonds formed
by eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 471
Score = 50.8 bits (122), Expect = 5e-08
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 15/75 (20%)
Query: 74 IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKK 133
+ SG KCP+DPN ++ ++ LYSGT +F D IFR + G +
Sbjct: 116 LESGRGKCPFDPNQPFASVLIDG-------ELYSGTAIDFMGRDAAIFR------SLGHR 162
Query: 134 EYTFKRTIKYDSKWL 148
Y RT +YDS+WL
Sbjct: 163 HYI--RTEQYDSRWL 175
>gnl|CDD|200530 cd11269, Sema_6D, The Sema domain, a protein interacting module, of
semaphorin 6D (Sema6D). Sema6D is expressed
predominantly in the nervous system during embryogenesis
and it uses Plexin-A1 as a receptor. It displays
repellent activity for dorsal root ganglion axons.
Sema6D also acts as a regulator of late phase primary
immune responses. In addition, Sema6D is overexpressed
in gastric carcinoma, indicating that it may have an
important role in the occurrence and development of the
cancer. Sema6D is a member of the class 6 semaphorin
family of proteins, which are membrane associated
semaphorins. Semaphorins are regulatory molecules
involved in the development of the nervous system and in
axonal guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 465
Score = 50.0 bits (119), Expect = 9e-08
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CP+D + A++ + LYS T A+F +D VI+R+
Sbjct: 113 SGLARCPFDARQTNVALFADG-------KLYSATVADFLASDAVIYRSMGDGSAL----- 160
Query: 136 TFKRTIKYDSKWL 148
RTIKYDSKW+
Sbjct: 161 ---RTIKYDSKWI 170
>gnl|CDD|200515 cd11254, Sema_3F, The Sema domain, a protein interacting module, of
semaphorin 3F (Sema3F). Sema3F is coexpressed with
semaphorin3B. Both Sema3B and Sema3F proteins are
candidate tumor suppressors that are down-regulated in
highly metastatic tumors. Two receptor families, the
neuropilins and plexins, have been implicated in
mediating the actions of semaphorins 3B and 3F. Sema3F
is a member of the class 3 semaphorin family of
proteins. Semaphorins are regulatory molecules in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 470
Score = 49.8 bits (119), Expect = 1e-07
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 16/80 (20%)
Query: 71 VPG-IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFT 129
P + SG KCPYDP +S + + LY+G +F D IFR T
Sbjct: 112 EPDKLESGKGKCPYDPKQDSVSALING-------ELYAGVYIDFMGTDAAIFR------T 158
Query: 130 TGKKEYTFKRTIKYDSKWLD 149
GK+ RT +Y+S+WL+
Sbjct: 159 MGKQ--PAMRTDQYNSRWLN 176
>gnl|CDD|200502 cd11241, Sema_5, The Sema domain, a protein interacting module, of
semaphorin 5 (Sema5). Class 5 semaphorins are
transmembrane glycoproteins characterized by unique
thrombospondin specific repeats in the extracellular
region of the protein. There are three subfamilies in
class 5 semaphorins, namely 5A, 5B and 5C. Sema5A and
Sema5B function as guidance cues for optic and
corticofugal nerve development, respectively.
Sema5A-induced cell migration requires Met signaling.
Sema5C is an early development gene and may play a role
in odor-guided behavior. Sema5A is also implicated in
cancer. In a screening model for metastasis, the
Drosophila Sema5A ortholog, Dsema-5C, has been found to
be required in tumorigenicity and metastasis. Sema5A is
highly expressed in human pancreatic cancer cells and is
associated with tumor growth, invasion and metastasis.
Semaphorins are regulatory molecules involved in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 438
Score = 49.1 bits (117), Expect = 2e-07
Identities = 33/103 (32%), Positives = 47/103 (45%), Gaps = 25/103 (24%)
Query: 49 FTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSG 108
F+ V + L N LT + SG+A+CPY P NSTA+ G LY+G
Sbjct: 87 FSPVCTIRKLSN-LTQI-LDTI-----SGVARCPYSPAHNSTALISASG------ELYAG 133
Query: 109 TNAEFTKADTVIFRT--DLLNFTTGKKEYTFKRTIKYDSKWLD 149
T +F+ D I+R+ RT +Y+SKWL+
Sbjct: 134 TVYDFSGRDPAIYRSLGGKPPL----------RTAQYNSKWLN 166
>gnl|CDD|200531 cd11270, Sema_6E, The Sema domain, a protein interacting module,
semaphorin 6E (sema6E). Sema6E is expressed
predominantly in the nervous system during
embryogenesis. It binds Plexin A1 and might utilize it
as a receptor to repel axons of specific types during
development. Sema6E acts as a repellent to dorsal root
ganglion axons as well as sympathetic axons. Sema6E is a
member of the class 6 semaphorin family of proteins,
which are membrane associated semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 462
Score = 47.8 bits (113), Expect = 5e-07
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 14/73 (19%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
G A+CP++ ++ ++ G+ YS T +F +D VI+R+ G+
Sbjct: 110 IGQARCPFESRQSNVGLFAG----GDF---YSATMTDFLASDAVIYRS------LGESSP 156
Query: 136 TFKRTIKYDSKWL 148
RT+KYDSKWL
Sbjct: 157 VL-RTVKYDSKWL 168
>gnl|CDD|200524 cd11263, Sema_5A, The Sema domain, a protein interacting module, of
semaphorin 5A (Sema5A). Originally, mouse Sema5A was
identified as a protein that induces inhibitory
responses during optic nerve development. Recent studies
show that Sema5A controls innate immunity in mice. It
also has been identified as a candidate gene for causing
idiopathic autism in humans. Plexin B3 functions as a
binding partner and receptor for Sema5A. Furthermore,
Sema5A is also implicated in cancer. The role of the
Drosophila Sema5A ortholog, Dsema-5C, in tumorigenicity
and metastasis has been reported. Sema5A is highly
expressed in human pancreatic cancer cells and is
associated with tumor growth, invasion and metastasis.
Sema5A belongs to class 5 semaphorin family of proteins,
which are transmembrane glycoproteins characterized by
unique thrombospondin specific repeats in the
extracellular region of the protein. Semaphorins are
regulatory molecules involved in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 436
Score = 47.3 bits (112), Expect = 7e-07
Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 20/90 (22%)
Query: 60 NNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTV 119
NNLT + H+ + SG+A+CPY P NSTA+ G LY+ T +F D
Sbjct: 97 NNLTEI--HDQI----SGMARCPYSPQHNSTALLTSSGE------LYAATAMDFPGRDPA 144
Query: 120 IFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
I+R+ RT +Y+SKWL+
Sbjct: 145 IYRS--------LGILPPLRTAQYNSKWLN 166
>gnl|CDD|200527 cd11266, Sema_6A, The Sema domain, a protein interacting module, of
semaphorins 6A (Sema6A). In the cerebellum,
Sema6A-plexin A2 signaling modulates granule cell
migration by controlling centrosome positioning. Besides
plexin A2, plexin A4 is also found to be a receptor of
Sema6A. Interactions between plexin A2, plexin A4, and
Sema6A control lamina-restricted projection of
hippocampal mossy fibers. It is required for the
clustering of boundary cap cells at the PNS/CNS
interface and thus, prevents motoneurons from streaming
out of the ventral spinal cord. At the dorsal root entry
site, it organizes the segregation of dorsal roots.
Sema6A may also be involved in axonal pathfinding
processes in the periinfarct and homotopic contralateral
cortex. Sema6A is a member of the class 6 semaphorin
family of proteins, which are membrane associated
semaphorins. Semaphorins are regulatory molecules
involved in the development of the nervous system and in
axonal guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 466
Score = 46.6 bits (110), Expect = 1e-06
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CPYD + A++ + LYS T +F D VI+R+ +
Sbjct: 113 SGMARCPYDAKHANVALFADG-------KLYSATVTDFLAIDAVIYRS--------LGDS 157
Query: 136 TFKRTIKYDSKWL 148
RT+K+DSKWL
Sbjct: 158 PTLRTVKHDSKWL 170
>gnl|CDD|200529 cd11268, Sema_6C, The Sema domain, a protein interacting module, of
semaphorin 6C (Sema6C, also called semaphorin Y).
Sema6C is highly expressed in adult brain and skeletal
muscle and it shows growth cone collapsing activity. It
may play a role in the maintenance and remodelling of
neuronal connections. In adult skeletal muscle, this
role includes prevention of motor neuron sprouting and
uncontrolled motor neuron growth. The expression of
Sema6C in adult skeletal muscle is down-regulated
following denervation. Sema6C is a member of the class 6
semaphorin family of proteins, which are membrane
associated semaphorins. Semaphorins are regulatory
molecules involved in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 465
Score = 46.2 bits (109), Expect = 2e-06
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG A+CP+D ++ AI+ E +LYS T A+F +D V++R + G +
Sbjct: 112 SGQARCPFDATQSNVAIFAEG-------SLYSATAADFQASDAVVYR------SLGPQPP 158
Query: 136 TFKRTIKYDSKWL 148
R+ KYDSKWL
Sbjct: 159 L--RSAKYDSKWL 169
>gnl|CDD|200528 cd11267, Sema_6B, The Sema domain, a protein interacting module, of
semaphorin 6B (Sema6B). Sema6B functions as repellents
for axon growth; this repulsive activity is mediated by
its receptor Plexin A4. Sema6B is expressed in CA3, and
repels mossy fibers in a Plexin A4 dependent manner. In
human, it was shown that peroxisome
proliferator-activated receptors (PPARs) and
9-cis-retinoic acid receptor (RXR) regulate human
semaphorin 6B (Sema6B) gene expression. Sema6B is a
member of the class 6 semaphorin family of proteins,
which are membrane associated semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 466
Score = 45.2 bits (107), Expect = 3e-06
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG+A+CPYDP + A++ + L++ T +F D VI+R+ +
Sbjct: 113 SGMARCPYDPKHANVALFADG-------MLFTATVTDFLAIDAVIYRS--------LGDS 157
Query: 136 TFKRTIKYDSKW 147
RT+K+DSKW
Sbjct: 158 PALRTVKHDSKW 169
>gnl|CDD|214747 smart00630, Sema, semaphorin domain.
Length = 390
Score = 42.0 bits (99), Expect = 5e-05
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 101 NLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFK 152
NL LY GT A+F+ +D I R+ + G RT+ YDSKWL+
Sbjct: 90 NLGELYVGTVADFSGSDPAIPRSLSVRRLKGTSGV-SLRTVLYDSKWLNEPN 140
>gnl|CDD|200510 cd11249, Sema_3A, The Sema domain, a protein interacting module, of
semaphorin 3A (Sema3A). Sema3A has been reported to
inhibit the growth of certain experimental tumors and to
regulate endothelial cell migration and apoptosis in
vitro, as well as arteriogenesis in the muscle, skin
vessel permeability, and tumor angiogenesis in vivo. The
function of Sema3A is mediated through receptors
neuropilin-1 (NP1) and plexins, although little is known
about the requirement of specific plexins in its
receptor complex. It is known however that Plexin-A4 is
the receptor for Sema3A in the Toll-like receptor- and
sepsis-induced cytokine storm during immune response.
Sema3A is a member of the Class 3 semaphorin family of
secreted proteins. Semaphorins are regulatory molecules
in the development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 493
Score = 38.8 bits (90), Expect = 6e-04
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 15/84 (17%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
+G K PYDP + ++ ++ LYSGT A+F D IFR T G
Sbjct: 139 NGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFR------TLGHHHP 185
Query: 136 TFKRTIKYDSKWLDSFKSLIAKII 159
RT ++DS+WL+ + + A +I
Sbjct: 186 I--RTEQHDSRWLNDPRFISAHLI 207
>gnl|CDD|200501 cd11240, Sema_4, The Sema domain, a protein interacting module, of
class 4 semaphorins (Sema4). Class 4 semaphorins
(Sema4s) are transmembrane regulator molecules involved
in the development of the nervous system, immune
response, cytoskeletal organization, angiogenesis, and
cell-cell interactions. There are 7 distinct subfamilies
in class 4 semaphorins, named 4A to 4G. Several class 4
subfamilies play important roles in the immune system
and are called "immune semaphorins". Sema4A plays
critical roles in T cell-DC interactions in the immune
response. Sema4D/CD100, expressed by lymphocytes,
promotes the aggregation and survival of B lymphocytes
and inhibits cytokine-induced migration of immune cells
in vitro. It is required for normal activation of B and
T lymphocytes. Sema4B negatively regulates basophil
functions through T cell-basophil contacts and
significantly inhibits IL-4 and IL-6 production from
basophils in response to various stimuli, including IL-3
and papain. Sema4s not only influence the activation
state of cells but also modulate their migration and
survival. The effects of Sema4s on nonlymphoid cells are
mediated by plexin D1 and plexin Bs. The Sema4G and
Sema4C genes are expressed in the developing cerebellar
cortex and are involved in neural tube closure and
development of cerebellar granules cells through
receptor plexin B2. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 37.8 bits (88), Expect = 0.001
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
G +CP+DP TAI V+ LYS T F ++ VI R
Sbjct: 112 DGKGRCPFDPAQRYTAIMVDG-------ELYSATVNNFLGSEPVISRN 152
>gnl|CDD|200511 cd11250, Sema_3B, The Sema domain, a protein interacting module, of
semaphorin 3B (Sema3B). Sema3B is coexpressed with
semaphorin 3F and both proteins are candidate tumor
suppressors. Both Sema3B and Sema3F show high levels of
expression in normal tissues and low-grade tumors but
are down-regulated in highly metastatic tumors in the
lung, melanoma cells, bladder carcinoma cells and
prostate carcinoma. They are upregulated by estrogen and
inhibit cell motility and invasiveness through decreased
FAK phosphorylation and inhibition of MMP-2 and MMP-9
expression. Two receptor families, the neuropilins (NP)
and plexins, have been implicated in mediating the
actions of semaphorins 3B and 3F. Sema3B is a member of
the class 3 semaphorin family of proteins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 471
Score = 37.2 bits (86), Expect = 0.002
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYT 136
G K PYDP + ++ V LYSG + D IFR + G++
Sbjct: 119 GKGKSPYDPRHTAASVLVGD-------ELYSGVATDLMGRDFTIFR------SLGQRPSL 165
Query: 137 FKRTIKYDSKWLDSFK 152
RT ++DS+WL+ K
Sbjct: 166 --RTEQHDSRWLNEPK 179
>gnl|CDD|200518 cd11257, Sema_4B, The Sema domain, a protein interacting module, of
semaphorin 4B (Sema4B). Sema4B, expressed in T and B
cells, is an immune semaphorin. It functions as a
negative regulatory of basophils through T cell-basophil
contacts and it significantly inhibits IL-4 and IL-6
production from basophils in response to various
stimuli, including IL-3 and papain. In addition, T
cell-derived Sema4B suppresses basophil-mediated Th2
skewing and humoral memory responses. Sema4B may be also
involved in lung cancer cell mobility by inducing the
degradation of CLCP1 (CUB, LCCL-homology, coagulation
factor V/VIII homology domains protein). Sema4B is
characterized by a PDZ-binding motif at the
carboxy-terminus, which mediates interaction with the
post-synaptic density protein PSD-95/SAP90, which is
thought to play a central role during synaptogenesis and
in the structure and function of post-synaptic
specializations of excitatory synapses. Sema4B belongs
to class 4 transmembrane semaphorin family proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 464
Score = 36.8 bits (85), Expect = 0.002
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
G +CP+DP STAI V+ LY+GT + F D +I+R+
Sbjct: 120 GKGRCPFDPEYKSTAIMVDG-------ELYTGTVSNFQGNDPIIYRS 159
>gnl|CDD|200517 cd11256, Sema_4A, The Sema domain, a protein interacting module, of
semaphorin 4A (Sema4A). Sema4A is expressed in immune
cells and is thus termed an "immune semaphorin". It
plays critical roles in T cell-DC interactions in the
immune response. It has been reported to enhance
activation and differentiation of T cells in vitro and
generation of antigen-specific T cells in vivo. The
function of Sema4A in the immune response implicates its
role in infectious and noninfectious diseases. Sema4A
exerts its function through three receptors, namely
Plexin B, Plexin D1, and Tim-2. Sema4A belongs to the
class 4 transmembrane semaphorin family of proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. TThe Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 447
Score = 35.7 bits (82), Expect = 0.007
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYT 136
G + P+DP N TAI V+ LY+GT F + +IFR L K
Sbjct: 119 GKGQSPFDPQHNYTAILVDG-------ELYTGTMNNFRGNEPIIFRN--LGTKVSLKTDG 169
Query: 137 FKRTIKYDSKWLDSFKS 153
F R + D+ ++ SF
Sbjct: 170 FLRWLNADAVFVASFNP 186
>gnl|CDD|200516 cd11255, Sema_3G, The Sema domain, a protein interacting module, of
semaphorin 3G (Sema3G). Semaphorin 3G is identified as
a primarily endothelial cell- expressed class 3
semaphorin that controls endothelial and smooth muscle
cell functions in autocrine and paracrine manners,
respectively. It is mainly expressed in the lung and
kidney, and a little in the brain. Semaphorins are
regulatory molecules in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 474
Score = 35.3 bits (81), Expect = 0.008
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 12/62 (19%)
Query: 67 RHEHV----PG-IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIF 121
R EHV P + SG +CP++P + + LY+G A+F D+VIF
Sbjct: 103 RGEHVFSLDPTTVESGRGRCPHEPKRPFASTFTGG-------ELYTGLTADFLGRDSVIF 155
Query: 122 RT 123
R
Sbjct: 156 RG 157
>gnl|CDD|200520 cd11259, Sema_4D, The Sema domain, a protein interacting module, of
semaphorin 4D (Sema4D, also known as CD100).
Sema4D/CD100 is expressed in immune cells and plays
critical roles in immune response; it is thus termed an
"immune semaphorin". It is expressed by lymphocytes and
promotes the aggregation and survival of B lymphocytes
and inhibits cytokine-induced migration of immune cells
in vitro. Sema4D/CD100 knock-out mice demonstrate that
Sema4D is required for normal activation of B and T
lymphocytes. Sema4D increases B-cell and DC function
using either Plexin B1 or CD72 as receptors. The
function of Sema4D in immune response implicates its
role in infectious and noninfectious diseases. Sema4D
belongs to the class 4 transmembrane semaphorin family
of proteins. Semaphorins are regulatory molecules in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 471
Score = 34.1 bits (78), Expect = 0.024
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 13/58 (22%)
Query: 65 LGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFR 122
LG++E G +CP+DP + T++ V+ LYSGT+ F ++ +I R
Sbjct: 116 LGKNE------DGKGRCPFDPAQSYTSVMVDG-------ELYSGTSYNFLGSEPIISR 160
>gnl|CDD|200519 cd11258, Sema_4C, The Sema domain, a protein interacting module, of
semaphorin 4C (Sema4C). Sema4C acts as a Plexin B2
ligand to regulate the development of cerebellar granule
cells and to modulate ureteric branching in the
developing kidney. The binding of Sema4C to Plexin B2
results the phosphorylation of downstream regulator
ErbB-2 and the plexin protein itself. The cytoplasmic
region of Sema4C binds a neurite-outgrowth-related
protein SFAP75, suggesting that Sema4C may also play a
role in neural function. Sema4C belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 458
Score = 33.2 bits (76), Expect = 0.038
Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFR 122
G KCPYDP T + V+ LYS T F + VI R
Sbjct: 114 GKGKCPYDPAKGHTGLIVDG-------ELYSATLNNFLGTEPVILR 152
>gnl|CDD|200512 cd11251, Sema_3C, The Sema domain, a protein interacting module, of
semaphorin 3C (Sema3C). Sema3C is a secreted semaphorin
expressed in and adjacent to cardiac neural crest cells,
and causes impaired migration of neural crest cells to
the developing cardiac outflow tract, resulting in the
interruption of the aortic arch and persistent truncus
arteriosus. It has been proposed that Sema3C acts as a
guidance molecule, regulating migration of neural crest
cells that express semaphorin receptors such as plexin
A2. Sema3C may also participate in tumor progression.
The cleavage of Sema3C induced by ADAMTS1 promotes the
migration of breast cancer cells. Sema3C is a member of
the class 3 semaphorin family of secreted proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 470
Score = 33.3 bits (76), Expect = 0.038
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 15/73 (20%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG +C ++PN N+ ++ + + L+SG +F D IFR+ T
Sbjct: 117 SGKGRCSFNPNVNTVSVMINE-------ELFSGMYIDFMGTDAAIFRS----LTKRNA-- 163
Query: 136 TFKRTIKYDSKWL 148
RT +++SKWL
Sbjct: 164 --VRTDQHNSKWL 174
>gnl|CDD|200521 cd11260, Sema_4E, The Sema domain, a protein interacting module, of
semaphorin 4E (Sema4E). Sema4E is expressed in the
epithelial cells that line the pharyngeal arches in
zebrafish. It may act as a guidance molecule to restrict
the branchiomotor axons to the mesenchymal cells.
Gain-of-function and loss-of-function studies
demonstrate that Sema4E is essential for the guidance of
facial axons from the hindbrain into their pharyngeal
arch targets and is sufficient for guidance of gill
motor axons. Sema4E guides facial motor axons by a
repulsive action. Sema4E belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulatory molecules involved in the development of
the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 456
Score = 33.0 bits (75), Expect = 0.054
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 7/47 (14%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
G KCP+DP +++ V++ LYS T+ F ++ VI R+
Sbjct: 113 GKGKCPFDPFQRYSSVMVDQ-------DLYSATSMNFLGSEPVIMRS 152
>gnl|CDD|200513 cd11252, Sema_3D, The Sema domain, a protein interacting module, of
semaphorin 3D (Sema3D). Sema3D is a secreted semaphorin
expressed during the development of the nervous system.
In zebrafish, Sema3D is expressed in the ventral tectum.
It guides retinal axons along the dorsoventral axis of
the tectum and guides the laterality of retinal ganglion
cell (RGC) projections. Both Sema3D knockdown or its
ubiquitous overexpression induced aberrant ipsilateral
projections. Proper balance of Sema3D is needed at the
midline for the progression of RGC axons from the chiasm
midline into the contralateral optic tract. Sema3D is a
member of the class 3 semaphorin family of proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 474
Score = 31.4 bits (71), Expect = 0.19
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 70 HVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
+ SG KCP+DP ++ ++ LY+GT ++F DT R+
Sbjct: 112 DTQNLESGRLKCPFDPQQPFASVMTDE-------YLYAGTASDFLGKDTTFTRS 158
>gnl|CDD|215220 PLN02393, PLN02393, leucoanthocyanidin dioxygenase like protein.
Length = 362
Score = 30.8 bits (70), Expect = 0.26
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 2 YSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVF 53
Y FL P S ++ + +P++PP ++++EE EE K KV
Sbjct: 145 YYFLHYLPSSLKDPNKWPSLPPSC------RELIEEYGEEVVKLCGRLMKVL 190
>gnl|CDD|200495 cd09295, Sema, The Sema domain, a protein interacting module, of
semaphorins and plexins. Both semaphorins and plexins
have a Sema domain on their N-termini. Plexins function
as receptors for the semaphorins. Evolutionarily,
plexins may be the ancestor of semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems,
and cancer. Semaphorins can be divided into 7 classes.
Vertebrates have members in classes 3-7, whereas classes
1 and 2 are known only in invertebrates. Class 2 and 3
semaphorins are secreted; classes 1 and 4 through 6 are
transmembrane proteins; and class 7 is membrane
associated via glycosylphosphatidylinositol (GPI)
linkage. Plexins are a large family of transmembrane
proteins, which are divided into four types (A-D)
according to sequence similarity. In vertebrates, type A
plexins serve as co-receptors for neuropilins to mediate
the signalling of class 3 semaphorins. Plexins serve as
direct receptors for several other members of the
semaphorin family: class 6 semaphorins signal through
type A plexins and class 4 semaphorins through type B
plexins. This family also includes the MET and RON
receptor tyrosine kinases. The Sema domain is located at
the N-terminus and contains four disulfide bonds formed
by eight conserved cysteine residues. It serves to
recognize and bind receptors.
Length = 392
Score = 28.7 bits (64), Expect = 1.2
Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 14/74 (18%)
Query: 76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
SG +CP D ++ + V+ LYS T+ +F D N
Sbjct: 109 SGRPRCPIDNKHSNMGVNVDS-------KLYSATDHDFKDGDRPALSRRSSNVHY----- 156
Query: 136 TFKRTIKYDSKWLD 149
R + S LD
Sbjct: 157 --LRIVVDSSTGLD 168
>gnl|CDD|238874 cd01836, FeeA_FeeB_like, SGNH_hydrolase subfamily, FeeA, FeeB and
similar esterases/lipases. FeeA and FeeB are part of a
biosynthetic gene cluster and may participate in the
biosynthesis of long-chain N-acyltyrosines by providing
saturated and unsaturated fatty acids, which it turn are
loaded onto the acyl carrier protein FeeL. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 191
Score = 28.4 bits (64), Expect = 1.2
Identities = 9/29 (31%), Positives = 12/29 (41%), Gaps = 5/29 (17%)
Query: 4 FLGLPPLSFENQHNFPAVPPQLATFFGVK 32
+PPL FPA+P L G +
Sbjct: 111 VTAVPPL-----GRFPALPQPLRWLLGRR 134
>gnl|CDD|201810 pfam01466, Skp1, Skp1 family, dimerisation domain.
Length = 78
Score = 26.8 bits (60), Expect = 1.7
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 22 PPQLATFFGVKKVVEEEEEEEKKKE 46
P ++ FG++ EEEEE +KE
Sbjct: 48 PEEIREIFGIENDFTPEEEEEIRKE 72
>gnl|CDD|200522 cd11261, Sema_4F, The Sema domain, a protein interacting module, of
semaphorin 4F (Sema4F). Sema4F plays role in
heterotypic cell-cell contacts and controls cell
proliferation and suppresses tumorigenesis. In
neurofibromatosis type 1 (NF1) patients, reduced Sema4F
level disrupts Schwann cell/axonal interactions.
Experiments using a yeast two-hybrid system show that
the extreme C-terminus of Sema4F interacts with the PDZ
domains of post-synaptic density protein SAP90/PSD-95,
indicating possible functional involvement of Semas4F at
glutamatergic synapses. Recent work also suggests a role
for Sema4F in the injury response of intramedullary
axotomized motoneuron. Sema4F belongs to the class 4
transmembrane semaphorin family of proteins. Semaphorins
are regulator molecules involved in the development of
the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 460
Score = 28.3 bits (63), Expect = 1.7
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 65 LGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFR 122
+ + V + SG KCP++P S AI LY+ T F + +I R
Sbjct: 103 VSSFQQVERLESGRGKCPFEPAQRSAAIMAGG-------VLYAATVKNFLGTEPIISR 153
>gnl|CDD|200523 cd11262, Sema_4G, The Sema domain, a protein interacting module, of
semaphorin 4G (Sema4G). The Sema4G and Sema4C genes are
expressed in the developing cerebellar cortex. Sema4G
and Sema4C proteins specifically bind to Plexin B2
expressed in the cerebellar granule cells. Sema4G and
Sema4C are involved in neural tube closure and
cerebellar granule cell development through Plexin
B2.Sema4G belongs to the class 4 transmembrane
semaphorin family of proteins. Semaphorins are
regulatory molecules involved in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 457
Score = 28.2 bits (63), Expect = 2.2
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 77 GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEF 113
G KCPYDP T + V+ LY+ + EF
Sbjct: 113 GKEKCPYDPAKGYTGLIVDGQ-------LYTASQYEF 142
>gnl|CDD|162974 TIGR02683, upstrm_HI1419, putative addiction module killer protein.
Members of this strictly bacterial protein family are
small, at roughly 100 amino acids. The gene is almost
invariably the upstream member of a gene pair, where the
downstream member is a predicted DNA-binding protein
from a clade within Pfam helix-turn-helix family
pfam01381. These gene pairs, when found on the bacterial
chromosome, often are located with prophage regions, but
also in both integrated plasmid regions and near
housekeeping genes. Analysis suggests that the gene pair
may serve as an addiction module.
Length = 95
Score = 26.8 bits (60), Expect = 2.4
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 135 YTFKRTIKYDSKWLDSFKSLIAKI 158
YT RT +D KWLD K AK
Sbjct: 1 YTIDRTDTFD-KWLDGLKDPRAKA 23
>gnl|CDD|213299 cd05933, ACSBG_like, Bubblegum-like very long-chain fatty acid CoA
synthetase (VL-FACS). This family of very long-chain
fatty acid CoA synthetase is named bubblegum because
Drosophila melanogaster mutant bubblegum (BGM) has
elevated levels of very-long-chain fatty acids (VLCFA)
caused by a defective gene of this family. The human
homolog (hsBG) has been characterized as a very long
chain fatty acid CoA synthetase that functions
specifically in the brain; hsBG may play a central role
in brain VLCFA metabolism and myelinogenesis. VL-FACS is
involved in the first reaction step of very long chain
fatty acid degradation. It catalyzes the formation of
fatty acyl-CoA in a two-step reaction: the formation of
a fatty acyl-AMP molecule as an intermediate, and the
formation of a fatty acyl-CoA. Free fatty acids must be
"activated" to their CoA thioesters before participating
in most catabolic and anabolic reactions.
Length = 594
Score = 28.1 bits (63), Expect = 2.6
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 27 TFFGVKKVVEEEEEEEKK---KERGFT-KVFFW---KILENNLTHLGRHEHVPGIGSGIA 79
F GV +V E+ +E K K G K+ W LE NL +G P +A
Sbjct: 245 AFMGVPRVWEKIQERMKAVGAKSTGLKRKIASWAKGVGLETNLKLMGGESPPPM-CFRLA 303
Query: 80 KC 81
K
Sbjct: 304 KK 305
>gnl|CDD|224726 COG1813, COG1813, Predicted transcription factor, homolog of
eukaryotic MBF1 [Transcription].
Length = 165
Score = 26.6 bits (59), Expect = 4.7
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 24 QLATFFGVK---KVVEEEEEEEKKKERGFT 50
+L G+K KV EEEE + K + G T
Sbjct: 126 KLEKLLGIKLVEKVDEEEEGPKGKDDDGLT 155
>gnl|CDD|200514 cd11253, Sema_3E, The Sema domain, a protein interacting module, of
semaphorin 3E (Sema3E). Sema3E is a secreted molecule
implicated in axonal path finding and inhibition of
developmental and postischemic angiogenesis. It is also
highly expressed in metastatic cancer cells. Sema3E
signaling, through its high affinity functional receptor
Plexin D1, drives cancer cell invasiveness and
metastatic spreading. Sema3E is a member of the class 3
semaphorin family of proteins. Semaphorins are
regulatory molecules in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 471
Score = 27.1 bits (60), Expect = 4.8
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 15/68 (22%)
Query: 58 LENNLTHLGRHEHVPGIGSGIAKCPYDPNDN--STAIWVEKGNPGNLPALYSGTNAEFTK 115
E++L L + G +CP+DPN + ST I E L+ G +++
Sbjct: 103 SEDHLFQLESDK----FERGRGRCPFDPNSSFISTLIGGE---------LFVGLYSDYWG 149
Query: 116 ADTVIFRT 123
D IFRT
Sbjct: 150 RDAAIFRT 157
>gnl|CDD|220184 pfam09332, Mcm10, Mcm10 replication factor. Mcm10 is a eukaryotic
DNA replication factor that regulates the stability and
chromatin association of DNA polymerase alpha.
Length = 346
Score = 26.8 bits (59), Expect = 5.9
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 36 EEEEEEEKKKERGFTKVFFWKILENNLTH 64
E+EE KK R F KIL +H
Sbjct: 187 PEDEEPAMKKRRYLESEEFQKILAAKSSH 215
>gnl|CDD|204918 pfam12436, USP7, Ubiquitin-specific protease 7. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam00443, pfam00917. USP7 regulates
the turnover of p53.
Length = 35
Score = 24.4 bits (54), Expect = 6.1
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 36 EEEEEEEKKKER 47
E EE E ++KER
Sbjct: 16 EREERERRRKER 27
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 26.8 bits (60), Expect = 6.3
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 24 QLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILE 59
+LA G +V+ ++ K K+ F I +
Sbjct: 203 ELAKELGADEVLNSLDDSPKDKKAAGLGGGFDVIFD 238
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 25.5 bits (56), Expect = 7.4
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 20 AVPPQLATFFGVKKVVEEEEEEEKKKE 46
A A +K E+++EEEK++E
Sbjct: 68 AAAAAAAEEKAEEKEEEKKKEEEKEEE 94
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin.
Trichoplein or mitostatin, was first defined as a
meiosis-specific nuclear structural protein. It has
since been linked with mitochondrial movement. It is
associated with the mitochondrial outer membrane, and
over-expression leads to reduction in mitochondrial
motility whereas lack of it enhances mitochondrial
movement. The activity appears to be mediated through
binding the mitochondria to the actin intermediate
filaments (IFs).
Length = 349
Score = 26.4 bits (59), Expect = 8.6
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 31 VKKVVEEEEEEEKKKER 47
+K + EEEE E K+KE
Sbjct: 52 LKALAEEEERERKRKEE 68
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
0.317 0.137 0.418
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,474,005
Number of extensions: 768735
Number of successful extensions: 1085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1035
Number of HSP's successfully gapped: 51
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 55 (25.0 bits)