RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5392
(100 letters)
>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 = 226 bits (579), Expect = 1e-74
Identities = 78/99 (78%), Positives = 90/99 (90%)
Query: 1 MDPIIYREPLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARV 60
DP+IYREPL+TE+YD LNAPNFVSS GD+VYFFFRETAVE+INCGKA+YSRVARV
Sbjct: 138 ADPLIYREPLRTERYDLKQLNAPNFVSSFAYGDYVYFFFRETAVEYINCGKAIYSRVARV 197
Query: 61 CKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
CK D+GGPH FR+RWTSFLK+RLNCSVPG++PFYF+EIQ
Sbjct: 198 CKNDKGGPHPFRDRWTSFLKARLNCSVPGEYPFYFNEIQ 236
>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 = 169 bits (429), Expect = 2e-52
Identities = 67/103 (65%), Positives = 80/103 (77%), Gaps = 5/103 (4%)
Query: 2 DPIIYR-----EPLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
DP+IYR PL+TE +DS LN P FV + GD+VYFFFRE AVE+INCGKAVYSR
Sbjct: 136 DPVIYRTLGHNPPLRTEYHDSKWLNEPQFVGAFDIGDYVYFFFREIAVEYINCGKAVYSR 195
Query: 57 VARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
VARVCK D+GG +WT+FLK+RLNCSVPG+FPFYF+E+Q
Sbjct: 196 VARVCKNDQGGSRSLEKKWTTFLKARLNCSVPGEFPFYFNELQ 238
>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 = 162 bits (411), Expect = 9e-50
Identities = 61/106 (57%), Positives = 77/106 (72%), Gaps = 8/106 (7%)
Query: 2 DPIIYREP-------LQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVY 54
D IYR L+T+QY+S LN P FV S G+FVYF FRE+AVE++NCGK +Y
Sbjct: 142 DSAIYRTLGTSNKSFLRTKQYNSKWLNEPQFVGSFETGNFVYFLFRESAVEYMNCGKVIY 201
Query: 55 SRVARVCKYDRGG-PHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
SR+ARVCK D GG ++ WT+FLK+RLNCS+PG++PFYFDEIQ
Sbjct: 202 SRIARVCKNDVGGGTMLLKDNWTTFLKARLNCSLPGEYPFYFDEIQ 247
>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 = 159 bits (404), Expect = 1e-48
Identities = 66/110 (60%), Positives = 79/110 (71%), Gaps = 12/110 (10%)
Query: 2 DPIIYREPL------------QTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINC 49
+ +IYR PL +T +YDS L+ PNFV S GD+VYFFFRETAVE+INC
Sbjct: 152 NTVIYRPPLYNNTKGRHESFMRTLKYDSKWLDEPNFVGSFDIGDYVYFFFRETAVEYINC 211
Query: 50 GKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
GK VYSRVARVCK D GG + R WT+FLK+RLNCS+ G+FPFYF+EIQ
Sbjct: 212 GKVVYSRVARVCKKDTGGKNVLRQNWTTFLKARLNCSISGEFPFYFNEIQ 261
>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 = 155 bits (393), Expect = 3e-47
Identities = 61/103 (59%), Positives = 74/103 (71%), Gaps = 5/103 (4%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
DP IYR PL+T QY+S LN PNFV S G+ YFFFRE AVE +CGK VYSR
Sbjct: 142 DPAIYRSLGGKPPLRTAQYNSKWLNEPNFVGSYEIGNHTYFFFRENAVEHQDCGKTVYSR 201
Query: 57 VARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
+ARVCK D GG + WT+F+K+RLNCS+PG+FPFY++EIQ
Sbjct: 202 IARVCKNDIGGRFLLEDTWTTFMKARLNCSLPGEFPFYYNEIQ 244
>gnl|CDD|214747 smart00630, Sema, semaphorin domain.
Length = 390
Score = 142 bits (359), Expect = 2e-42
Identities = 66/110 (60%), Positives = 74/110 (67%), Gaps = 12/110 (10%)
Query: 2 DPIIYRE------------PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINC 49
DP I R L+T YDS LN PNFV + GDFVYFFFRETAVE NC
Sbjct: 106 DPAIPRSLSVRRLKGTSGVSLRTVLYDSKWLNEPNFVYAFESGDFVYFFFRETAVEDDNC 165
Query: 50 GKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
GKAV+SRVARVCK D GGP +WTSFLK+RL CSVPG+ PFYF+E+Q
Sbjct: 166 GKAVHSRVARVCKNDVGGPRSLDKKWTSFLKARLECSVPGEDPFYFNELQ 215
>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 = 134 bits (339), Expect = 3e-39
Identities = 63/113 (55%), Positives = 73/113 (64%), Gaps = 16/113 (14%)
Query: 2 DPIIYR-----EPLQTEQYDSMSLNAPNFVSSL-------TQGDFVYFFFRETAVEFINC 49
DP I R + L+TE +DS LN PNFV S D VYFFFRETAVE NC
Sbjct: 141 DPSIRRLLGSYDGLRTEFHDSKLLNLPNFVDSYPIHYVHSFSDDKVYFFFRETAVEDSNC 200
Query: 50 GKAVYSRVARVCKYDRGGPHRFR-NRWTSFLKSRLNCSVPG--DFPFYFDEIQ 99
KA++SRVARVCK D GG N+WT+FLK+RLNCSVPG PFYF+E+Q
Sbjct: 201 -KAIHSRVARVCKNDPGGRSYLELNKWTTFLKARLNCSVPGREGIPFYFNELQ 252
>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 = 131 bits (330), Expect = 9e-38
Identities = 60/104 (57%), Positives = 72/104 (69%), Gaps = 6/104 (5%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
D +IYR L+T +YDS L P+FV ++ GD+VYFFFRE AVE+ GK V+SR
Sbjct: 147 DAVIYRSLGDSPTLRTVKYDSKWLKEPHFVHAVEYGDYVYFFFREIAVEYNTLGKVVFSR 206
Query: 57 VARVCKYDRGGPHRFRNR-WTSFLKSRLNCSVPGDFPFYFDEIQ 99
VARVCK D GG R + WTSFLK+RLNCSVPGD FYFD +Q
Sbjct: 207 VARVCKNDMGGSPRVLEKQWTSFLKARLNCSVPGDSHFYFDVLQ 250
>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 = 128 bits (323), Expect = 6e-37
Identities = 60/103 (58%), Positives = 73/103 (70%), Gaps = 6/103 (5%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
DP IYR PL+T QY+S LN PNFVSS G+F YFFFRE AVE +CGK V+SR
Sbjct: 142 DPAIYRSLGILPPLRTAQYNSKWLNEPNFVSSYDIGNFTYFFFRENAVEH-DCGKTVFSR 200
Query: 57 VARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
ARVCK D GG + WT+F+K+RLNCS PG+ PFY++E+Q
Sbjct: 201 AARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEIPFYYNELQ 243
>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 = 127 bits (320), Expect = 2e-36
Identities = 59/103 (57%), Positives = 73/103 (70%), Gaps = 6/103 (5%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
DP IYR PL+T QY+S LN PNF+++ G F YFFFRE AVE +CGK VYSR
Sbjct: 142 DPAIYRSLGSVPPLRTAQYNSKWLNEPNFIAAYDIGLFTYFFFRENAVEH-DCGKTVYSR 200
Query: 57 VARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
VARVCK D GG + WT+F+K+RLNCS PG+ PFY++E+Q
Sbjct: 201 VARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEIPFYYNELQ 243
>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 = 121 bits (305), Expect = 3e-34
Identities = 59/104 (56%), Positives = 72/104 (69%), Gaps = 6/104 (5%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
D +IYR L+T +YDS + P+F+ ++ G++VYFFFRE AVE N GKAVYSR
Sbjct: 147 DAVIYRSMGDGSALRTIKYDSKWIKEPHFLHAIEYGNYVYFFFREIAVEHNNLGKAVYSR 206
Query: 57 VARVCKYDRGGPHR-FRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
VAR+CK D GG R WTSFLK+RLNCSVPGD FYFD +Q
Sbjct: 207 VARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQ 250
>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 = 114 bits (286), Expect = 1e-31
Identities = 58/104 (55%), Positives = 70/104 (67%), Gaps = 6/104 (5%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSR 56
D ++YR PL++ +YDS L P+FV +L GD VYFFFRE +VE G+ +SR
Sbjct: 146 DAVVYRSLGPQPPLRSAKYDSKWLREPHFVQALEHGDHVYFFFREVSVEDARLGRVQFSR 205
Query: 57 VARVCKYDRGGPHRFRNR-WTSFLKSRLNCSVPGDFPFYFDEIQ 99
VARVCK D GG R +R WTSFLK RLNCSVPGD FYFD +Q
Sbjct: 206 VARVCKRDMGGSPRALDRHWTSFLKLRLNCSVPGDSTFYFDVLQ 249
>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 = 113 bits (284), Expect = 3e-31
Identities = 55/105 (52%), Positives = 72/105 (68%), Gaps = 6/105 (5%)
Query: 1 MDPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYS 55
+D +IYR L+T ++DS L P FV ++ GD++YFFFRE AVE+ + GK V+
Sbjct: 146 IDAVIYRSLGDSPTLRTVKHDSKWLKEPYFVQAVDYGDYIYFFFREIAVEYNSMGKVVFP 205
Query: 56 RVARVCKYDRGGPHR-FRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
RVA+VCK D GG R +WTSFLK+RLNCSVPGD FYF+ +Q
Sbjct: 206 RVAQVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNILQ 250
>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 = 112 bits (281), Expect = 1e-30
Identities = 55/105 (52%), Positives = 67/105 (63%), Gaps = 6/105 (5%)
Query: 1 MDPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYS 55
+D +IYR L+T ++DS P FV ++ G VYFFFRE A+EF K V S
Sbjct: 146 IDAVIYRSLGDSPALRTVKHDSKWFKEPYFVHAVEWGSHVYFFFREIAMEFNYLEKVVVS 205
Query: 56 RVARVCKYDRGGPHR-FRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
RVARVCK D GG R +WTSFLK+RLNCSVPGD FYF+ +Q
Sbjct: 206 RVARVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNVLQ 250
>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 = 109 bits (272), Expect = 1e-29
Identities = 56/105 (53%), Positives = 69/105 (65%), Gaps = 7/105 (6%)
Query: 2 DPIIYRE------PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYS 55
D +IYR L+T +YDS L P+F+ ++ G++VYFF E AVE+ GK V+S
Sbjct: 144 DAVIYRSLGESSPVLRTVKYDSKWLREPHFLHAIEYGNYVYFFLSEIAVEYTTLGKVVFS 203
Query: 56 RVARVCKYDRGG-PHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
RVARVCK D GG P WTSFLK+RLNCSVPGD FYFD +Q
Sbjct: 204 RVARVCKNDNGGSPRVLERYWTSFLKARLNCSVPGDSFFYFDVLQ 248
>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 = 107 bits (268), Expect = 7e-29
Identities = 52/102 (50%), Positives = 63/102 (61%), Gaps = 9/102 (8%)
Query: 7 REPLQTEQYDSMSLNAPNFVSSLT-------QGDFVYFFFRETAVEFINCGKAVYSRVAR 59
R ++TEQYDS LN P FV + D VYFFFRE AVE GKA+YSRV R
Sbjct: 162 RHYIRTEQYDSRWLNEPKFVGAYLIPDSDNPDDDKVYFFFREKAVEAEGSGKAIYSRVGR 221
Query: 60 VCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD--FPFYFDEIQ 99
+CK D GG N+W++FLK+RL CSVPG YFDE++
Sbjct: 222 ICKNDVGGQRSLVNKWSTFLKARLVCSVPGPDGIDTYFDELE 263
>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 = 94.6 bits (235), Expect = 3e-24
Identities = 49/102 (48%), Positives = 63/102 (61%), Gaps = 9/102 (8%)
Query: 7 REPLQTEQYDSMSLNAPNFV-------SSLTQGDFVYFFFRETAVEFINCGKAVYSRVAR 59
R L+TEQ+DS LN P FV S D +YFFFRETAVE GK YSR+ +
Sbjct: 162 RPSLRTEQHDSRWLNEPKFVKVFWIPESENPDDDKIYFFFRETAVEAAGLGKQSYSRIGQ 221
Query: 60 VCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD--FPFYFDEIQ 99
+C+ D GG N+WT+FLK+RL CSVPG+ +FDE++
Sbjct: 222 ICRNDMGGQRSLVNKWTTFLKARLVCSVPGNEGGDTHFDELR 263
>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 = 91.4 bits (227), Expect = 3e-23
Identities = 47/112 (41%), Positives = 63/112 (56%), Gaps = 15/112 (13%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFV-------SSLTQGDFVYFFFRETAVEFINC 49
D I+R ++T+QY+S LN P FV SS D +YFFFRE ++E
Sbjct: 152 DAAIFRTMGKQPAMRTDQYNSRWLNDPAFVHAHLIPDSSEKNDDKLYFFFREKSLEAPQ- 210
Query: 50 GKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD--FPFYFDEIQ 99
AV SR+ RVC D GG N+W++FLK+RL CSVPG +FDE++
Sbjct: 211 SPAVLSRIGRVCLNDDGGHCCLVNKWSTFLKARLVCSVPGADGIETHFDELR 262
>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 = 91.2 bits (226), Expect = 5e-23
Identities = 45/100 (45%), Positives = 65/100 (65%), Gaps = 9/100 (9%)
Query: 9 PLQTEQYDSMSLNAPNFVSSL-------TQGDFVYFFFRETAVEFINCGKAVYSRVARVC 61
P++TEQ+DS LN P F+S+ + D +YFFFRE A++ + GKA ++R+ ++C
Sbjct: 185 PIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKIYFFFRENAIDGEHTGKATHARIGQLC 244
Query: 62 KYDRGGPHRFRNRWTSFLKSRLNCSVPG--DFPFYFDEIQ 99
K D GG N+WT+FLK+RL CSVPG +FDE+Q
Sbjct: 245 KNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQ 284
>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 = 86.8 bits (215), Expect = 2e-21
Identities = 44/112 (39%), Positives = 59/112 (52%), Gaps = 14/112 (12%)
Query: 2 DPIIYR-----EPLQTEQYDSMSLNAPNFVSSLT-------QGDFVYFFFRETAVEFINC 49
D I+R ++TE D L P FV S + VYFFF E A+E
Sbjct: 151 DAAIFRTMNHLAHIRTEHDDERLLKEPKFVGSYMIPDNEDPDDNKVYFFFTEKALEAEGG 210
Query: 50 GKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPG--DFPFYFDEIQ 99
A+Y+RV RVC D+GG N+W++FLK+RL CSVPG +FDE++
Sbjct: 211 NHAIYTRVGRVCANDQGGQRMLVNKWSTFLKTRLICSVPGPNGIDTHFDELE 262
>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 = 85.9 bits (213), Expect = 3e-21
Identities = 45/107 (42%), Positives = 54/107 (50%), Gaps = 17/107 (15%)
Query: 3 PIIYR-----EPLQTEQYDSMSLNAPNFVSS----------LTQGDFVYFFFRETAVEFI 47
P+I R L+TE LN P FV S D +YFFF ETAVE+
Sbjct: 147 PVISRNHSEGNVLKTE-NTLRWLNEPAFVGSAHIRESIDSPDGDDDKIYFFFTETAVEYD 205
Query: 48 NCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPG-DFPF 93
K SRVARVCK D GG + +WT+FLK++L CS P PF
Sbjct: 206 FYEKVTVSRVARVCKGDLGGQRTLQKKWTTFLKAQLVCSQPDSGLPF 252
>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 = 84.5 bits (209), Expect = 1e-20
Identities = 44/113 (38%), Positives = 65/113 (57%), Gaps = 17/113 (15%)
Query: 2 DPIIYR-----EPLQTEQYDSMSLNAPNFVSS----------LTQGDFVYFFFRETAVEF 46
+P+I R ++TE Y + LN P+FV S D +YFFF E AVE+
Sbjct: 147 EPVILRNLGQHYSMKTE-YLAFWLNEPHFVGSAFVPESVGSFTGDDDKIYFFFSERAVEY 205
Query: 47 INCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFDEIQ 99
+ V +RVARVCK D GG + +WT+FLK+RL CS+P ++ YF++++
Sbjct: 206 DCDSEQVVARVARVCKGDLGGARTLQKKWTTFLKARLLCSIP-EWQLYFNQLK 257
>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 = 81.5 bits (201), Expect = 1e-19
Identities = 45/100 (45%), Positives = 60/100 (60%), Gaps = 14/100 (14%)
Query: 2 DPIIYR---EPLQTEQYDSMSLNAPNFVS--SLTQG--------DFVYFFFRETAVEFIN 48
+P+I R ++TE + S LN PNF+ ++ + D +Y FF ETAVE+
Sbjct: 146 EPVIMRSSPITIRTE-FKSSWLNEPNFIYMAAVPESEDSPEGDDDKIYLFFSETAVEYDF 204
Query: 49 CGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVP 88
K V SRVARVCK D GG + +WTSFLK+RL+CSVP
Sbjct: 205 YNKLVVSRVARVCKGDLGGQRTLQKKWTSFLKARLDCSVP 244
>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 = 81.4 bits (201), Expect = 1e-19
Identities = 51/111 (45%), Positives = 60/111 (54%), Gaps = 23/111 (20%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLN---APNFVSSL--------TQG--DFVYFFFRETA 43
DPIIYR PL+TE SLN P FV S G D +YFFF ET
Sbjct: 153 DPIIYRSLGSGTPLKTEN----SLNWLQDPAFVGSAYIQESLPKLVGDDDKIYFFFSETG 208
Query: 44 VEFINCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD-FPF 93
EF + SR+ARVCK D GG + RWT+FLK++L CS+P D FPF
Sbjct: 209 KEFDFFENTIVSRIARVCKGDEGGERVLQKRWTTFLKAQLLCSLPDDGFPF 259
>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 = 81.1 bits (200), Expect = 2e-19
Identities = 45/101 (44%), Positives = 59/101 (58%), Gaps = 15/101 (14%)
Query: 2 DPIIYR----EPLQTEQYDSMSLNAPNFV----------SSLTQGDFVYFFFRETAVEFI 47
+PII R PL+TE Y LN P+FV S + D +YFFF E +VE+
Sbjct: 155 EPIISRNSSQSPLRTE-YAIPWLNEPSFVFADVIRADPDSPDGEDDKIYFFFTEVSVEYE 213
Query: 48 NCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVP 88
GK + R+ARVCK D+GG + +WTSFLK+RL CS+P
Sbjct: 214 FVGKLLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSIP 254
>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 = 79.2 bits (195), Expect = 7e-19
Identities = 42/99 (42%), Positives = 54/99 (54%), Gaps = 7/99 (7%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSL--TQGDFVYFFFRETAVEFINCGKAVY 54
+PII+R L+T+ + FV+S VYFFF ETA EF K
Sbjct: 152 EPIIFRNLGTKVSLKTDGFLRWLNADAVFVASFNPQGDSKVYFFFEETAREFDFFEKLTV 211
Query: 55 SRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPF 93
+RVARVCK D GG + +WT+FLK++L CS G FPF
Sbjct: 212 ARVARVCKNDVGGEKLLQKKWTTFLKAQLTCSQQGHFPF 250
>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 = 78.8 bits (194), Expect = 9e-19
Identities = 39/96 (40%), Positives = 50/96 (52%), Gaps = 8/96 (8%)
Query: 2 DPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQG---DFVYFFFRETAVEFINCGKAV 53
P + R L+ S L+ FV + G D VYFFFR+ VE++ G
Sbjct: 144 RPALSRRSSNVHYLRIVVDSSTGLDEITFVYAFVSGDDDDEVYFFFRQEPVEYLKKGMVY 203
Query: 54 YSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPG 89
R+ARVCK D GG HR + + TSFLK+ LNCS P
Sbjct: 204 VPRIARVCKLDVGGCHRLKKKLTSFLKADLNCSRPQ 239
>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 = 77.6 bits (191), Expect = 3e-18
Identities = 35/69 (50%), Positives = 45/69 (65%), Gaps = 2/69 (2%)
Query: 33 DFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD-- 90
D +YFFFRE + + K+V SRV RVCK D GG N+WT+FLK+RL CS+PG
Sbjct: 198 DKIYFFFREASQDGSTSDKSVLSRVGRVCKNDVGGQRSLINKWTTFLKARLVCSIPGPDG 257
Query: 91 FPFYFDEIQ 99
+FDE+Q
Sbjct: 258 ADTHFDELQ 266
>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 = 73.8 bits (181), Expect = 6e-17
Identities = 41/103 (39%), Positives = 58/103 (56%), Gaps = 11/103 (10%)
Query: 7 REPLQTEQYDSMSLNAPNFV-------SSLTQGDFVYFFFRETAVEF-INCGKAVYSRVA 58
R PL+TE D L+ P FV ++ D VYFFF E A E + A++SRV
Sbjct: 161 RSPLRTET-DQRLLHEPRFVAAHLIPDNADRDNDKVYFFFTERATETAEDDDGAIHSRVG 219
Query: 59 RVCKYDRGGPHRFRNRWTSFLKSRLNCSVPG--DFPFYFDEIQ 99
R+C D GG N+W++F+K+RL CSVPG +FD+++
Sbjct: 220 RLCANDAGGQRVLVNKWSTFIKARLVCSVPGPHGIQTHFDQLE 262
>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 = 71.8 bits (176), Expect = 3e-16
Identities = 36/102 (35%), Positives = 56/102 (54%), Gaps = 9/102 (8%)
Query: 7 REPLQTEQYDSMSLNAPNFVSSLTQGD-------FVYFFFRETAVEFINCGKAVYSRVAR 59
R ++T+Q++S L+ P FV + D +YFF +E + K ++S +AR
Sbjct: 161 RNAVRTDQHNSKWLSEPIFVDAHLIPDGTDPNDAKLYFFLKERLTDNSGSTKQIHSMIAR 220
Query: 60 VCKYDRGGPHRFRNRWTSFLKSRLNCSVPGD--FPFYFDEIQ 99
VC D GG N+WT+FLK+RL CSV + +FDE++
Sbjct: 221 VCPNDTGGQRSLVNKWTTFLKARLVCSVMDEDGTETHFDELE 262
>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 = 68.6 bits (168), Expect = 4e-15
Identities = 39/98 (39%), Positives = 56/98 (57%), Gaps = 12/98 (12%)
Query: 10 LQTEQYDSMSLNAPNFV----------SSLTQGDFVYFFFRETAVE-FINCGKAVYSRVA 58
L+TE+ + LN +FV SS+ D +YFFF E + E ++ +RVA
Sbjct: 157 LRTEEAPTRWLNDADFVGSVLVRESMNSSVGDDDKIYFFFTERSQEETAYFSQSRVARVA 216
Query: 59 RVCKYDRGGPHRFRNRWTSFLKSRLNCSVPGDFPFYFD 96
RVCK DRGG + +WTSFLK+RL C +P ++ F F+
Sbjct: 217 RVCKGDRGGKKTLQRKWTSFLKARLVCYIP-EYEFLFN 253
>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 = 68.0 bits (166), Expect = 8e-15
Identities = 39/102 (38%), Positives = 53/102 (51%), Gaps = 15/102 (14%)
Query: 2 DPIIYREPLQTEQY----DSMS-LNAPNFVSSLT----------QGDFVYFFFRETAVEF 46
+PII R + E++ S LNAP FV+++ D +YFFF ETA E+
Sbjct: 148 EPIISRAVGRAEEWIRTETLPSWLNAPAFVAAVFLSPAEWGDEDGDDEIYFFFTETAREY 207
Query: 47 INCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLNCSVP 88
+ + RVARVC D GG + RWT+FLK+ L C P
Sbjct: 208 DSYERIKVPRVARVCAGDLGGRKTLQQRWTTFLKADLLCPGP 249
>gnl|CDD|200504 cd11243, Sema_7A, The Sema domain, a protein interacting module, of
semaphorin 7A (Sema7A, also called CD108). Sema7A plays
regulatory roles in both immune and nervous systems.
Unlike other semaphorins, which act as repulsive
guidance cues, Sema7A enhances central and peripheral
axon growth and is required for proper axon tract
formation during embryonic development. Sema7A also
plays a critical role in the negative regulation of T
cell activation and function. Sema7A is a
membrane-anchored 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 = 414
Score = 49.5 bits (118), Expect = 3e-08
Identities = 31/85 (36%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 23 PNFVSSLT------QGDFVYFFFRETAVEFINCGKAVY-SRVARVCKYDRGG-PHRFRNR 74
P FV + D +Y+FFRE E SRVAR+CK D+GG ++
Sbjct: 151 PQFVKATLLPEDEQYQDKIYYFFREDN-EDKGPEAEPNISRVARLCKEDQGGTSSLSTSK 209
Query: 75 WTSFLKSRLNCSVPGDFPFYFDEIQ 99
W++FLK+RL C P P F+ +Q
Sbjct: 210 WSTFLKARLVCGDPAT-PMNFNRLQ 233
>gnl|CDD|200497 cd11236, Sema_plexin_like, The Sema domain, a protein interacting
module, of Plexins and MET-like receptor tyrosine
kinases. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestor of semaphorins. Ligand binding activates signal
transduction pathways controlling axon guidance in the
nervous system and other developmental processes
including cell migration and morphogenesis, immune
function, and tumor progression. Plexins are divided
into four types (A-D) according to sequence similarity.
In vertebrates, type A Plexins serve as the co-receptors
for neuropilins to mediate the signalling of class 3
semaphorins except Sema3E, which signals through Plexin
D1. 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. Plexin C1 serves as the receptor of
Sema7A and plays regulation roles in both immune and
nervous systems. 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 as a ligand-recognition and -binding module.
Length = 401
Score = 29.2 bits (66), Expect = 0.27
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 24 NFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKYDRG 66
+V + G F YF + + ++ SR+ RVC+ D
Sbjct: 184 KYVYGFSSGGFSYFVTVQR--KSVDDESPYISRLVRVCQSDSN 224
>gnl|CDD|225511 COG2963, COG2963, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 116
Score = 28.0 bits (62), Expect = 0.56
Identities = 9/46 (19%), Positives = 13/46 (28%), Gaps = 2/46 (4%)
Query: 39 FRETAVEFINCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRLN 84
F+ AV G S VAR ++ + K
Sbjct: 12 FKLEAVALYLRGGDTVSEVAR--EFGIVSATQLYKWRIQLQKGGGL 55
>gnl|CDD|200537 cd11276, Sema_plexin_B2, The Sema domain, a protein interacting
module, of Plexin B2. Plexin B2 serves as the receptor
of Sema4C and Sema4G. By signaling the effect of Sema4C
and Sema4G, the plexin B2 receptor plays important roles
in neural tube closure and cerebellar granule cell
development. Mice lacking Plexin B2 demonstrated defects
in closure of the neural tube and disorganization of the
embryonic brain. In developing kidney, Sema4C-Plexin B2
signaling modulates ureteric branching. Plexin B2 is
expressed both in the pretubular aggregates and the
ureteric epithelium in the developing kidney. Deletion
of Plexin B2 results in renal hypoplasia and occasional
double ureters. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 449
Score = 27.8 bits (62), Expect = 0.79
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 24 NFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPHRFRNRWTSFLKSRL 83
F + ++VYF F + + + +AR+C+ D + + S+ + L
Sbjct: 191 QFRYAFEDNNYVYFLFNQQ----LGHPDKNRTLIARLCEND--------HHYYSYTEMDL 238
Query: 84 NCSVP 88
NC
Sbjct: 239 NCRDG 243
>gnl|CDD|177870 PLN02225, PLN02225, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 701
Score = 27.0 bits (59), Expect = 2.0
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 13 EQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFIN-CGKAVYSRVARVCKYDRG--GP 68
E+ S++A + + S Q ++ FRE A GK +Y A+V +Y RG GP
Sbjct: 258 EEGSKASISALSSIMSKIQSSKIFRKFRELAKAMTKRIGKGMYEWAAKVDEYARGMVGP 316
>gnl|CDD|240448 cd13425, Peptidase_G1_like, Peptidases of the G1 family and
homologs that might lack peptidase activity. Some
members of this family had been classified earlier as
carboxyl peptidases insensitive to pepstatin, and the
family has also been called the eqolisin family, due to
the fact that the conserved catalytic dyad of the family
consists of a glutamate (E) and glutamine (Q) residue.
The family is found in fungi and bacteria. This family
also includes homologous uncharacterized proteins that
might lack peptidase activity.
Length = 195
Score = 26.6 bits (58), Expect = 2.1
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 22 APNFVSSLTQGDFVYFFFRETAVEFINC 49
A +FVS +Q D + F VEF NC
Sbjct: 130 AEDFVSYESQRDAIKATFS---VEFTNC 154
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 26.6 bits (59), Expect = 2.2
Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 60 VCKYDRGGPHRFRNRWTSFLK 80
+C+YD+ R +N+W LK
Sbjct: 292 LCQYDK--VQRSKNKWKCTLK 310
>gnl|CDD|234024 TIGR02817, adh_fam_1, zinc-binding alcohol dehydrogenase family
protein. Members of this model form a distinct subset
of the larger family of oxidoreductases that includes
zinc-binding alcohol dehydrogenases and NADPH:quinone
reductases (pfam00107). While some current members of
this family carry designations as putative alginate
lyase, it seems no sequence with a direct
characterization as such is detected by this model
[Energy metabolism, Fermentation].
Length = 336
Score = 25.9 bits (57), Expect = 4.2
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 4 IIYREPLQTEQYDSMSLNAPNFVSSLTQGD 33
I + +PL+ Q + + L A ++V SLT D
Sbjct: 199 IDHSKPLK-AQLEKLGLEAVSYVFSLTHTD 227
>gnl|CDD|200538 cd11277, Sema_plexin_B3, The Sema domain, a protein interacting
module, of Plexin B3. Plexin B3 is the receptor of
semaphorin 5A. It is a highly potent stimulator of
neurite outgrowth of primary murine cerebellar neurons.
Plexin B3 has been linked to verbal performance and
white matter volume in human brain. Furthermore, Sema5A
and plexin B3 have been implicated in the progression of
various types of cancer. They play an important role in
the invasion and metastasis of gastric carcinoma. The
stimulation of plexin B3 by Sema5A binding in human
glioma cells results in the inhibition of cell migration
and invasion. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 434
Score = 25.2 bits (55), Expect = 6.7
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 25 FVSSLTQGDFVYFFFRETAVEFINCGKAVY-SRVARVCKYD 64
+V + +VYF FR +A Y + VARVC D
Sbjct: 188 YVGAFAHNGYVYFLFRRRGAR----AQAEYRTYVARVCLGD 224
>gnl|CDD|227601 COG5276, COG5276, Uncharacterized conserved protein [Function
unknown].
Length = 370
Score = 25.2 bits (55), Expect = 8.0
Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 40 RETAVEFINCGKAVYSRVARVCKYDRGGPH-RFRNRWTSFLKSRL 83
ET+ V A V +G P N + FL S L
Sbjct: 252 YETSNPVSISTVPVSGEYAYVADGAKGLPIIDISNPPSPFLSSSL 296
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
0.327 0.142 0.454
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: 5,139,626
Number of extensions: 402682
Number of successful extensions: 418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 45
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)