RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10772
(378 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 = 382 bits (982), Expect = e-130
Identities = 147/221 (66%), Positives = 178/221 (80%), Gaps = 8/221 (3%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
+P+FVGS+DIG YV+FFFRETAVEYINCGK V+SRVARVCK+DTGGKN+L QNW T+LKA
Sbjct: 184 EPNFVGSFDIGDYVYFFFRETAVEYINCGKVVYSRVARVCKKDTGGKNVLRQNWTTFLKA 243
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVPG-DDTKFYGVFTTSTTGLMGSAICSFSIEDIERAF- 152
RLNCSI GEFPFYFNEIQ +YKVPG DDT FY FTTS G GSA+C F++ DI AF
Sbjct: 244 RLNCSISGEFPFYFNEIQSVYKVPGRDDTLFYATFTTSENGFTGSAVCVFTLSDINAAFD 303
Query: 153 VGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHRDN 212
GKFKEQA+S+SAWLPVLSS VPEPRPG CVND+ TL D+VL+F R+HPLMD+AV+H
Sbjct: 304 TGKFKEQASSSSAWLPVLSSEVPEPRPGTCVNDSATLSDTVLHFARTHPLMDDAVSH--G 361
Query: 213 KPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAATTTLR 253
P+ Y RD++FTHLVVD ++ + EY+V++A + +
Sbjct: 362 PPLLYLRDVVFTHLVVDKLRIDD----QEYVVFYAGSNDGK 398
Score = 28.9 bits (65), Expect = 5.3
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 1 MEISRTHRSLYVASDERIKQIALV 24
ME+ LYVASD R+ QI L
Sbjct: 430 MELLP-GEFLYVASDHRVSQIDLA 452
>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 = 303 bits (778), Expect = e-100
Identities = 128/219 (58%), Positives = 157/219 (71%), Gaps = 8/219 (3%)
Query: 36 PDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKAR 95
P FVG++DIG YV+FFFRE AVEYINCGK+V+SRVARVCK D GG L + W T+LKAR
Sbjct: 162 PQFVGAFDIGDYVYFFFREIAVEYINCGKAVYSRVARVCKNDQGGSRSLEKKWTTFLKAR 221
Query: 96 LNCSIPGEFPFYFNEIQDIYKVP---GDDTKFYGVFTTSTTGLMGSAICSFSIEDIERAF 152
LNCS+PGEFPFYFNE+QD++ +P + FY VFTT + GSA+C++S+ DIE F
Sbjct: 222 LNCSVPGEFPFYFNELQDVFDLPSPSNKEKIFYAVFTTPYNSIPGSAVCAYSLSDIEAVF 281
Query: 153 VGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHRDN 212
G FKEQ +S SAWLPV RVPEPRPG CV+D+ LPD LNFI+SHPLMDEAV N
Sbjct: 282 NGPFKEQHSSNSAWLPVPDERVPEPRPGTCVDDSSPLPDDTLNFIKSHPLMDEAVTPILN 341
Query: 213 KPVFYRRDLL--FTHLVVDVVQYEVFGTTSEYIVYFAAT 249
+P+F + D+ FT + VD VQ ++ T Y V F T
Sbjct: 342 RPLFIKTDVNYRFTKIAVDRVQAKLGQT---YDVLFVGT 377
Score = 32.4 bits (74), Expect = 0.40
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 1 MEISRTHRSLYVASDERIKQIALV 24
M++SR RSLYV S+ + Q+ L
Sbjct: 414 MQLSRKRRSLYVGSETGVLQVPLA 437
>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 = 286 bits (735), Expect = 1e-93
Identities = 116/203 (57%), Positives = 140/203 (68%), Gaps = 8/203 (3%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
P+FV S+ G YV+FFFRETAVEYINCGK+++SRVARVCK D GG + W ++LKA
Sbjct: 159 APNFVSSFAYGDYVYFFFRETAVEYINCGKAIYSRVARVCKNDKGGPHPFRDRWTSFLKA 218
Query: 95 RLNCSIPGEFPFYFNEIQDIYK-VPG-----DDTKFYGVFTTSTTGLMGSAICSFSIEDI 148
RLNCS+PGE+PFYFNEIQ V G YGVFTT + GSA+C+FS++DI
Sbjct: 219 RLNCSVPGEYPFYFNEIQSTSDIVEGGYGGKSAKLIYGVFTTPVNSISGSAVCAFSLQDI 278
Query: 149 ERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVA 208
F G FKEQ S WLPV S++VPEPRPGQCVND+ TLPD +NFI+SHPLMDEAV
Sbjct: 279 LEVFDGSFKEQQDINSNWLPVPSNKVPEPRPGQCVNDSRTLPDVTVNFIKSHPLMDEAVP 338
Query: 209 HRDNKPVFYRRDLL--FTHLVVD 229
+P+ R L FT + VD
Sbjct: 339 SFFGRPILVRTSLQYRFTQIAVD 361
>gnl|CDD|214747 smart00630, Sema, semaphorin domain.
Length = 390
Score = 268 bits (687), Expect = 4e-87
Identities = 117/238 (49%), Positives = 149/238 (62%), Gaps = 15/238 (6%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
+P+FV +++ G +V+FFFRETAVE NCGK+V SRVARVCK D GG L + W ++LKA
Sbjct: 138 EPNFVYAFESGDFVYFFFRETAVEDDNCGKAVHSRVARVCKNDVGGPRSLDKKWTSFLKA 197
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVP---GDDTKFYGVFTTSTTGLMGSAICSFSIEDIERA 151
RL CS+PGE PFYFNE+Q + +P D YGVF+TS+ + GSA+C+FS+ DI
Sbjct: 198 RLECSVPGEDPFYFNELQAAFLLPPGSESDDVLYGVFSTSSNPIPGSAVCAFSLSDINAV 257
Query: 152 FVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVN---DTETLPDSVLNFIRSHPLMDEAVA 208
F G FKE TSTS WLP +VP PRPG C N ++ LPD LNFI+SHPLMDE V
Sbjct: 258 FNGPFKECETSTSQWLPYSRGKVPYPRPGTCPNKPPSSKDLPDETLNFIKSHPLMDEVVQ 317
Query: 209 HRDNKPVFYRRDL--LFTHLVVDVVQYEVFGTTSEYIVYFAATTTLRTVFVKVRLLQD 264
+P+F + D L T + VD V T Y V F T+ R +KV L +
Sbjct: 318 PLTGRPLFVKTDSNYLLTSIAVDRVA-----TDGNYTVLFLGTSDGR--ILKVVLSES 368
>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 = 244 bits (626), Expect = 2e-77
Identities = 111/230 (48%), Positives = 134/230 (58%), Gaps = 22/230 (9%)
Query: 36 PDFVGSYDIGK-------YVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQN- 87
P+FV SY I V+FFFRETAVE NC K++ SRVARVCK D GG++ L N
Sbjct: 167 PNFVDSYPIHYVHSFSDDKVYFFFRETAVEDSNC-KAIHSRVARVCKNDPGGRSYLELNK 225
Query: 88 WATYLKARLNCSIPG--EFPFYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICS 142
W T+LKARLNCS+PG PFYFNE+Q + +P YGVFTTS+ GSA+C+
Sbjct: 226 WTTFLKARLNCSVPGREGIPFYFNELQAAFVLPTGADTDPVLYGVFTTSSNSSAGSAVCA 285
Query: 143 FSIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTET-LPDSVLNFIRSHP 201
FS+ DI + F G FK Q S WLP +VP PRPGQC N + LPD LNFIR HP
Sbjct: 286 FSMSDINQVFNGPFKHQEGPNSKWLPY-RGKVPYPRPGQCPNASNGDLPDDTLNFIRCHP 344
Query: 202 LMDEAVAHRDNKPVFYRRDL--LFTHLVVDVVQYEVFGTTSEYIVYFAAT 249
LMDE V N P+F + T + VD V+ +Y V F T
Sbjct: 345 LMDEVVPPLHNVPLFVGQSGNYRLTSIAVDRVEAG----DGQYTVLFLGT 390
>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 = 220 bits (563), Expect = 8e-68
Identities = 107/227 (47%), Positives = 136/227 (59%), Gaps = 21/227 (9%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGG-KNILSQNWATYLK 93
+P FV + + G YV+FFFRE AVEY GK VFSRVARVCK D GG +L + W ++LK
Sbjct: 172 EPHFVHAVEYGDYVYFFFREIAVEYNTLGKVVFSRVARVCKNDMGGSPRVLEKQWTSFLK 231
Query: 94 ARLNCSIPGEFPFYFNEIQ---DIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIER 150
ARLNCS+PG+ FYF+ +Q D+ ++ G GVFTT + GSA+C+F ++DIE+
Sbjct: 232 ARLNCSVPGDSHFYFDVLQAVTDVIRINGRPVVL-GVFTTQYNSIPGSAVCAFDMDDIEK 290
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCV--------NDTETLPDSVLNFIRSHPL 202
F G+FKEQ + SAW PV RVP+PRPG C + PD LNFI++HPL
Sbjct: 291 VFEGRFKEQKSPDSAWTPVPEDRVPKPRPGCCAGSGSAEKYKTSNDFPDDTLNFIKTHPL 350
Query: 203 MDEAVAHRDNKPVFYR---RDLLFTHLVVDVVQYEVFGTTSEYIVYF 246
MDEAV N+P F R R L T + VD G Y V F
Sbjct: 351 MDEAVPSIINRPWFTRTMVRYRL-TQIAVDNAA----GPYQNYTVVF 392
>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 = 210 bits (535), Expect = 6e-64
Identities = 100/233 (42%), Positives = 136/233 (58%), Gaps = 15/233 (6%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
+P+FVGSY+IG + +FFFRE AVE+ +CGK+V+SR+ARVCK D GG+ +L W T++KA
Sbjct: 167 EPNFVGSYEIGNHTYFFFRENAVEHQDCGKTVYSRIARVCKNDIGGRFLLEDTWTTFMKA 226
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVG 154
RLNCS+PGEFPFY+NEIQ + +P D Y VFTT+ G+ GSAIC+F++ I +AF G
Sbjct: 227 RLNCSLPGEFPFYYNEIQGTFYLPETDL-IYAVFTTNVNGIAGSAICAFNLSAINQAFNG 285
Query: 155 KFKEQATSTSAWLPVLSSRVPEPRPGQCVNDT------ETLPDSVLNFIRSHPLMDEAVA 208
FK Q + SAWLP P P P + + L + + LM E V
Sbjct: 286 PFKYQENNGSAWLP-----TPNPHPNFQCTTSIDRGQPANTTERDLQDAQKYQLMAEVVQ 340
Query: 209 HRDNKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFA-ATTTLRTVFVKVR 260
P+ D+ F+ L VDVVQ GT +I Y T+ ++ R
Sbjct: 341 PVTKIPLVTMDDVRFSKLAVDVVQGR--GTQLVHIFYVGTDYGTILKMYQPHR 391
>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 = 204 bits (520), Expect = 9e-62
Identities = 94/227 (41%), Positives = 137/227 (60%), Gaps = 11/227 (4%)
Query: 36 PDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKN-ILSQNWATYLKA 94
P FVGS++ G +V+F FRE+AVEY+NCGK ++SR+ARVCK D GG +L NW T+LKA
Sbjct: 170 PQFVGSFETGNFVYFLFRESAVEYMNCGKVIYSRIARVCKNDVGGGTMLLKDNWTTFLKA 229
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVG 154
RLNCS+PGE+PFYF+EIQ + +P D+ Y FTT + GSA+C+F++ I AF G
Sbjct: 230 RLNCSLPGEYPFYFDEIQGMTYLP-DEGILYATFTTPENSIAGSAVCAFNLSSINAAFDG 288
Query: 155 KFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHRDNKP 214
FK Q +S +AW RV + + +L R + LMDEAV +P
Sbjct: 289 PFKHQESSGAAW-----ERVNVNHRDHFNQCSSSSSSHLLESSR-YQLMDEAVQPITLEP 342
Query: 215 VFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAATT-TLRTVFVKVR 260
+ + + F+H+ VDV+ ++ S +++Y A T ++ + V R
Sbjct: 343 LHHAKLERFSHIAVDVIPTKIH--QSVHVLYVATTGGLIKKISVLPR 387
>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 = 196 bits (501), Expect = 1e-58
Identities = 96/209 (45%), Positives = 127/209 (60%), Gaps = 15/209 (7%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGG-KNILSQNWATYLK 93
+P FV + + G +V+FFFRE A+E+ K V SRVARVCK D GG + +L + W ++LK
Sbjct: 172 EPYFVHAVEWGSHVYFFFREIAMEFNYLEKVVVSRVARVCKNDMGGSQRVLEKQWTSFLK 231
Query: 94 ARLNCSIPGEFPFYFNEIQ---DIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIER 150
ARLNCS+PG+ FYFN +Q DI + G VF+T T + GSA+C+F + +
Sbjct: 232 ARLNCSVPGDSHFYFNVLQAVSDILNLGGRPV-VLAVFSTPTNSIPGSAVCAFDMTQVAA 290
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCV------NDTETLPDSVLNFIRSHPLMD 204
F G+F+EQ + S W PV VP PRPG C N + TLPD VLNF+++HPLMD
Sbjct: 291 VFEGRFREQKSPESIWTPVPEELVPRPRPGCCAAPGMRYNSSSTLPDEVLNFVKTHPLMD 350
Query: 205 EAVAHRDNKPVFYR---RDLLFTHLVVDV 230
EAV + P R R L TH+VVD
Sbjct: 351 EAVPSLGHAPWIVRTMTRYQL-THMVVDT 378
>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 = 196 bits (499), Expect = 2e-58
Identities = 96/238 (40%), Positives = 131/238 (55%), Gaps = 28/238 (11%)
Query: 36 PDFVGSYDIGKY----------VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILS 85
P FVGS I + ++FFF ETAVEY K SRVARVCK D GG+ L
Sbjct: 171 PAFVGSAHIRESIDSPDGDDDKIYFFFTETAVEYDFYEKVTVSRVARVCKGDLGGQRTLQ 230
Query: 86 QNWATYLKARLNCSIPGEFPFYFNEIQDIYKVPGDD---TKFYGVFTTSTTGLMGSAICS 142
+ W T+LKA+L CS P FN ++D++ + D T FYGVFT+ SA+C+
Sbjct: 231 KKWTTFLKAQLVCSQPDS-GLPFNVLRDVFVLSPDSWDATIFYGVFTSQWNVSGLSAVCA 289
Query: 143 FSIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTET---------LPDSV 193
+S+EDI++ F GK+KE TS W + VP+PRPG C+ ++ LPD+V
Sbjct: 290 YSLEDIKKVFSGKYKEFNRETSKWSR-YTGPVPDPRPGACITNSARSQGITSSLNLPDNV 348
Query: 194 LNFIRSHPLMDEAVAHRDNKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAATTT 251
L F++ HPLMDE V H N+P+ + + +T + V VQ + G T Y V F T
Sbjct: 349 LTFVKDHPLMDEQV-HPINRPLLVKSGVNYTRIAVHRVQ-ALDGQT--YTVLFLGTED 402
>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 = 194 bits (495), Expect = 7e-58
Identities = 100/229 (43%), Positives = 139/229 (60%), Gaps = 19/229 (8%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGG-KNILSQNWATYLK 93
+P F+ + + G YV+FFFRE AVE+ N GK+V+SRVAR+CK D GG + +L ++W ++LK
Sbjct: 172 EPHFLHAIEYGNYVYFFFREIAVEHNNLGKAVYSRVARICKNDMGGSQRVLEKHWTSFLK 231
Query: 94 ARLNCSIPGEFPFYFNEIQ---DIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIER 150
ARLNCS+PG+ FYF+ +Q DI ++ G T GVFTT + GSA+C+FS++DIE+
Sbjct: 232 ARLNCSVPGDSFFYFDVLQSITDIIEINGIPT-VVGVFTTQLNSIPGSAVCAFSMDDIEK 290
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVND--------TETLPDSVLNFIRSHPL 202
F G+FKEQ T S W V +VP+PRPG C + PD L+FI+SHPL
Sbjct: 291 VFKGRFKEQKTPDSVWTAVPEDKVPKPRPGCCAKHGLAEAYKTSIDFPDETLSFIKSHPL 350
Query: 203 MDEAVAHRDNKPVFYRRDLLF--THLVVDVVQYEVFGTTSEYIVYFAAT 249
MD AV +P F + + + T + VD G Y V F +
Sbjct: 351 MDSAVPSIIEEPWFTKTRVRYRLTAIAVD----HAAGPHQNYTVIFVGS 395
>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 = 194 bits (494), Expect = 1e-57
Identities = 92/196 (46%), Positives = 121/196 (61%), Gaps = 13/196 (6%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGG-KNILSQNWATYLK 93
+P FV + D G Y++FFFRE AVEY + GK VF RVA+VCK D GG + +L + W ++LK
Sbjct: 172 EPYFVQAVDYGDYIYFFFREIAVEYNSMGKVVFPRVAQVCKNDMGGSQRVLEKQWTSFLK 231
Query: 94 ARLNCSIPGEFPFYFNEIQ---DIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIER 150
ARLNCS+PG+ FYFN +Q D+ + G D F+T + GSA+C++ + DI
Sbjct: 232 ARLNCSVPGDSHFYFNILQAVTDVIHINGRDVVL-ATFSTPYNSIPGSAVCAYDMLDIAS 290
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDT--------ETLPDSVLNFIRSHPL 202
F G+FKEQ + S W PV RVP+PRPG C + PD LNFI++HPL
Sbjct: 291 VFTGRFKEQKSPDSTWTPVPDERVPKPRPGCCAGSSSLEKYATSNEFPDDTLNFIKTHPL 350
Query: 203 MDEAVAHRDNKPVFYR 218
MDEAV N+P F R
Sbjct: 351 MDEAVPSIINRPWFLR 366
>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 = 191 bits (486), Expect = 7e-57
Identities = 98/207 (47%), Positives = 123/207 (59%), Gaps = 20/207 (9%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
+P+FV SYDIG + +FFFRE AVE+ +CGK+VFSR ARVCK D GG+ +L W T++KA
Sbjct: 167 EPNFVSSYDIGNFTYFFFRENAVEH-DCGKTVFSRAARVCKNDIGGRFLLEDTWTTFMKA 225
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVG 154
RLNCS PGE PFY+NE+Q + +P D YG+FTT+ + SA+C F++ I +AF G
Sbjct: 226 RLNCSRPGEIPFYYNELQSTFFLPELDL-IYGIFTTNVNSIAASAVCVFNLSAISQAFNG 284
Query: 155 KFKEQATSTSAWLPVLSSRVPEPRPG-QC--------VNDTETLPDSVLNFIRSHPLMDE 205
FK Q S SAWLP P P P QC VN TE FI LM E
Sbjct: 285 PFKYQENSRSAWLP-----YPNPNPNFQCGTMDQGLYVNLTERNLQDAQKFI----LMHE 335
Query: 206 AVAHRDNKPVFYRRDLLFTHLVVDVVQ 232
V P F + F+H+ VDVVQ
Sbjct: 336 VVQPVTPVPYFMEDNSRFSHVAVDVVQ 362
>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 = 191 bits (487), Expect = 2e-56
Identities = 92/227 (40%), Positives = 124/227 (54%), Gaps = 28/227 (12%)
Query: 36 PDFVGSYDI-------GKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNW 88
P FVG+Y I V+FFFRE AVE GK+++SRV R+CK D GG+ L W
Sbjct: 178 PKFVGAYLIPDSDNPDDDKVYFFFREKAVEAEGSGKAIYSRVGRICKNDVGGQRSLVNKW 237
Query: 89 ATYLKARLNCSIPGE--FPFYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSF 143
+T+LKARL CS+PG YF+E++D++ +P D K YGVFTTS+ GSA+C +
Sbjct: 238 STFLKARLVCSVPGPDGIDTYFDELEDVFLLPTRDPKNPLIYGVFTTSSNVFKGSAVCVY 297
Query: 144 SIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQC--------VNDTETLPDSVLN 195
S+ DI AF G F + W+ +VP PRPG C T+ PD V++
Sbjct: 298 SMADIRAAFNGPFAHKEGPNYQWVE-YQGKVPYPRPGTCPSKTYGPLYKSTKDFPDDVIS 356
Query: 196 FIRSHPLMDEAVAHRDNKPVFYRRDL--LFTHLVVDVV-----QYEV 235
F RSHPLM V +P+ R ++ T + VD V QY+V
Sbjct: 357 FARSHPLMYNPVYPLHGRPLLIRTNVPYRLTQIAVDRVEAEDGQYDV 403
>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 = 189 bits (481), Expect = 5e-56
Identities = 96/228 (42%), Positives = 135/228 (59%), Gaps = 18/228 (7%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKA 94
+P+F+ +YDIG + +FFFRE AVE+ +CGK+V+SRVARVCK D GG+ +L W T++KA
Sbjct: 167 EPNFIAAYDIGLFTYFFFRENAVEH-DCGKTVYSRVARVCKNDIGGRFLLEDTWTTFMKA 225
Query: 95 RLNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVG 154
RLNCS PGE PFY+NE+Q + +P D YGVFTT+ + SA+C+F++ I +AF G
Sbjct: 226 RLNCSRPGEIPFYYNELQSTFYLPEQDL-IYGVFTTNVNSIAASAVCAFNLSAITQAFNG 284
Query: 155 KFKEQATSTSAWLPVLSSRVPEPRPG-QC--VNDT---ETLPDSVLNFIRSHPLMDEAVA 208
F+ Q SAWLP P P QC ++D E L + L + LM++ V
Sbjct: 285 PFRYQENPRSAWLP-----TANPIPNFQCGTLSDDSPNENLTERSLQDAQRLFLMNDVVQ 339
Query: 209 HRDNKPVFYRRDLLFTHLVVDVVQ-----YEVFGTTSEYIVYFAATTT 251
P+ + + F+ LVVD+VQ Y V +EY A +T
Sbjct: 340 PVTVDPLVTQDSVRFSKLVVDIVQGKDTLYHVMYIGTEYGTILKALST 387
>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 = 183 bits (465), Expect = 2e-53
Identities = 93/208 (44%), Positives = 128/208 (61%), Gaps = 14/208 (6%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGK-NILSQNWATYLK 93
+P FV + + G +V+FFFRE +VE G+ FSRVARVCKRD GG L ++W ++LK
Sbjct: 171 EPHFVQALEHGDHVYFFFREVSVEDARLGRVQFSRVARVCKRDMGGSPRALDRHWTSFLK 230
Query: 94 ARLNCSIPGEFPFYFNEIQDI---YKVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIER 150
RLNCS+PG+ FYF+ +Q + + G + +GVFTT T + GSA+C+F +++IER
Sbjct: 231 LRLNCSVPGDSTFYFDVLQALTGPVNLHGR-SALFGVFTTQTNSIPGSAVCAFYLDEIER 289
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCV--------NDTETLPDSVLNFIRSHPL 202
F GKFKEQ + AW PV RVP PRPG C + + LPD VL FI++HPL
Sbjct: 290 GFEGKFKEQRSLDGAWTPVSEDRVPSPRPGSCAGVGGAALFSSSRDLPDDVLTFIKAHPL 349
Query: 203 MDEAVAHRDNKPVF-YRRDLLFTHLVVD 229
+D AV ++P+ L T + VD
Sbjct: 350 LDPAVPPVTHQPLLTLTSRALLTQVAVD 377
>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 = 182 bits (462), Expect = 4e-53
Identities = 105/262 (40%), Positives = 141/262 (53%), Gaps = 27/262 (10%)
Query: 35 QPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGK-NILSQNWATYLK 93
+P F+ + + G YV+FF E AVEY GK VFSRVARVCK D GG +L + W ++LK
Sbjct: 170 EPHFLHAIEYGNYVYFFLSEIAVEYTTLGKVVFSRVARVCKNDNGGSPRVLERYWTSFLK 229
Query: 94 ARLNCSIPGEFPFYFNEIQDIYKVPGDDTK--FYGVFTTSTTGLMGSAICSFSIEDIERA 151
ARLNCS+PG+ FYF+ +Q + V + + GVFTT + GSA+C+F ++DIE+
Sbjct: 230 ARLNCSVPGDSFFYFDVLQSLTNVMQINHRPAVLGVFTTQANSITGSAVCAFYMDDIEKV 289
Query: 152 FVGKFKEQATSTSAWLPVLSSRVPEPRPGQCV--------NDTETLPDSVLNFIRSHPLM 203
F GKFKEQ S SAW PV VP+PRPG C + PD L FI+S+PLM
Sbjct: 290 FNGKFKEQRNSESAWTPVPDEAVPKPRPGSCAGDGPAAGYKSSTNFPDETLTFIKSYPLM 349
Query: 204 DEAVAHRDNKPVFYRRDLLF--THLVVDVVQYEVFGTTSEYIVYFAATT----------T 251
DEAV +N+P F R F T + VD G Y V F +
Sbjct: 350 DEAVPSVNNRPCFTRTTSRFKLTQIAVDTAA----GPYKNYTVVFLGSENGHVLKVLASM 405
Query: 252 LRTVFVKVRLLQDVSNTSDSIC 273
++L+D+ + + C
Sbjct: 406 HPNSSYSTQVLEDIDVYNPNKC 427
>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 = 167 bits (425), Expect = 2e-47
Identities = 91/242 (37%), Positives = 129/242 (53%), Gaps = 21/242 (8%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGE--FP 105
++FFFRE + + KSV SRV RVCK D GG+ L W T+LKARL CSIPG
Sbjct: 200 IYFFFREASQDGSTSDKSVLSRVGRVCKNDVGGQRSLINKWTTFLKARLVCSIPGPDGAD 259
Query: 106 FYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATS 162
+F+E+QDI+ +P D + YGVFTT+++ GSA+C +S+ DI F G + + +
Sbjct: 260 THFDELQDIFLLPTRDERNPVVYGVFTTTSSIFKGSAVCVYSMADIRAVFNGPYAHKESP 319
Query: 163 TSAWLPVLSSRVPEPRPGQC--------VNDTETLPDSVLNFIRSHPLMDEAVAHRDNKP 214
W+ R+P PRPG C + T+ PD V++FI+ HPLM ++V P
Sbjct: 320 DHRWVQ-YEGRIPYPRPGTCPSKTYDPLIKSTKDFPDEVISFIKRHPLMYKSVYPLTGGP 378
Query: 215 VFYR--RDLLFTHLVVDVVQYEVFGTTSEYIVYFAATTTLRTVFVKVRLLQDVSNTSDSI 272
VF R D T +VVD V E +Y V F T + TV V + ++ + +
Sbjct: 379 VFTRINVDYRLTQIVVDHVAAE----DGQYDVMFLG-TDIGTVLKVVSITKEKWTMEEVV 433
Query: 273 CE 274
E
Sbjct: 434 LE 435
>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 = 166 bits (421), Expect = 6e-47
Identities = 81/227 (35%), Positives = 120/227 (52%), Gaps = 22/227 (9%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGE--FP 105
++FFFRETAVE GK +SR+ ++C+ D GG+ L W T+LKARL CS+PG
Sbjct: 197 IYFFFRETAVEAAGLGKQSYSRIGQICRNDMGGQRSLVNKWTTFLKARLVCSVPGNEGGD 256
Query: 106 FYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATS 162
+F+E++D++ + D + Y VF+TS++ GSA+C +++ D+ RAF+G F +
Sbjct: 257 THFDELRDVFLLQTRDKRNPLIYAVFSTSSSVFQGSAVCVYTMNDVRRAFLGPFAHKEGP 316
Query: 163 TSAWLPVLSSRVPEPRPGQC-------VNDTETLPDSVLNFIRSHPLMDEAVAHRDNKPV 215
W+ +VP PRPG C T+ PD V+ F R+HPLM V +P+
Sbjct: 317 NYQWVS-YQGKVPYPRPGMCPSKTFGSFESTKDFPDDVIQFARNHPLMFNPVLPLGGRPL 375
Query: 216 FYRR--DLLFTHLVVDVVQYEVFGTTSEYIVYFAAT---TTLRTVFV 257
F R FT + VD V Y V F T + L+ + V
Sbjct: 376 FLRTGIPYTFTQIAVD----RVAAADGHYDVMFIGTDVGSVLKVISV 418
>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 = 164 bits (418), Expect = 1e-46
Identities = 79/197 (40%), Positives = 118/197 (59%), Gaps = 15/197 (7%)
Query: 48 VFFFFRETAVEYINC-GKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGEFPF 106
++FFF E + E +S +RVARVCK D GGK L + W ++LKARL C IP E+ F
Sbjct: 192 IYFFFTERSQEETAYFSQSRVARVARVCKGDRGGKKTLQRKWTSFLKARLVCYIP-EYEF 250
Query: 107 YFNEIQDIYKVPG---DDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATST 163
FN ++ ++ + G DT FYG+F + SAIC +S+ DI+ AF G + E S+
Sbjct: 251 LFNVLRSVFVLWGSTPQDTVFYGIFGLEWKNVKASAICRYSLSDIQTAFEGPYMEYQDSS 310
Query: 164 SAWLPVLSSRVPEPRPGQCVND---------TETLPDSVLNFIRSHPLMDEAVAHRDNKP 214
S W + +VPEPRPG C+ D ++ LPD+VL+F+R HPLM E V + +P
Sbjct: 311 SKWSR-YTGKVPEPRPGSCITDEHRSQGINSSQDLPDNVLDFVRRHPLMAEQVLPVEGRP 369
Query: 215 VFYRRDLLFTHLVVDVV 231
+ ++R++++T + V V
Sbjct: 370 LLFKRNVIYTKIAVQTV 386
>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 = 163 bits (413), Expect = 7e-46
Identities = 91/246 (36%), Positives = 128/246 (52%), Gaps = 38/246 (15%)
Query: 32 NCLQ-PDFVGSYDI----GKYV------FFFFRETAVEYINCGKSVFSRVARVCKRDTGG 80
N LQ P FVGS I K V +FFF ET E+ ++ SR+ARVCK D GG
Sbjct: 173 NWLQDPAFVGSAYIQESLPKLVGDDDKIYFFFSETGKEFDFFENTIVSRIARVCKGDEGG 232
Query: 81 KNILSQNWATYLKARLNCSIPGE-FPFYFNEIQDIYKVPGD-----DTKFYGVFTT--ST 132
+ +L + W T+LKA+L CS+P + FP FN +QD++ + DT FYGVFT+
Sbjct: 233 ERVLQKRWTTFLKAQLLCSLPDDGFP--FNVLQDVFVLTPSPEDWKDTLFYGVFTSQWHK 290
Query: 133 TGLMGSAICSFSIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTET---- 188
SA+C F+++ ++RAF G +KE T W VPEPRPG C+ ++
Sbjct: 291 GTAGSSAVCVFTMDQVQRAFNGLYKEVNRETQQWYTYTHP-VPEPRPGACITNSARERKI 349
Query: 189 -----LPDSVLNFIRSHPLMDEAVAHRDNKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYI 243
+PD VLNF++ H LMD V + P+ + + +T + V V+ G Y
Sbjct: 350 NSSLHMPDRVLNFVKDHFLMDGQVRSQ---PLLLQPQVRYTQIAVHRVK----GLHKTYD 402
Query: 244 VYFAAT 249
V F T
Sbjct: 403 VLFLGT 408
>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 = 160 bits (407), Expect = 3e-45
Identities = 79/220 (35%), Positives = 115/220 (52%), Gaps = 14/220 (6%)
Query: 38 FVGSYDI--GKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKAR 95
FV S++ V+FFF ETA E+ K +RVARVCK D GG+ +L + W T+LKA+
Sbjct: 180 FVASFNPQGDSKVYFFFEETAREFDFFEKLTVARVARVCKNDVGGEKLLQKKWTTFLKAQ 239
Query: 96 LNCSIPGEFPFYFNEIQDIYKVPGDD---TKFYGVFTT--STTGLMGSAICSFSIEDIER 150
L CS G FP FN I + + D + FY VFT+ G SA+C++ + DIE+
Sbjct: 240 LTCSQQGHFP--FNVIHHVALLNQPDPNNSVFYAVFTSQWQLGGRRSSAVCAYKLNDIEK 297
Query: 151 AFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHR 210
F GK+KE +S W V +PRPG C + D LNF++ H LMDE V
Sbjct: 298 VFNGKYKELNKESSRW-TRYMGPVSDPRPGSCSGGKSS--DKALNFMKDHFLMDEVVLPG 354
Query: 211 DNKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAATT 250
+P+ + ++ +T + VD VQ + +++
Sbjct: 355 AGRPLLVKSNVQYTRIAVDSVQG--VSGHNYTVMFLGTDK 392
>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 = 160 bits (407), Expect = 4e-45
Identities = 84/201 (41%), Positives = 116/201 (57%), Gaps = 21/201 (10%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIP-GEFPF 106
++ FF ETAVEY K V SRVARVCK D GG+ L + W ++LKARL+CS+P P+
Sbjct: 191 IYLFFSETAVEYDFYNKLVVSRVARVCKGDLGGQRTLQKKWTSFLKARLDCSVPEPSLPY 250
Query: 107 YFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFV-GKFKEQA-- 160
IQD++ V D + FY VFT+ + SA+C++++ DI F GKFK
Sbjct: 251 V---IQDVFHVCHQDWRKCVFYAVFTSQSDSSQSSAVCAYNVTDISNVFSRGKFKTPVAV 307
Query: 161 -TSTSAWLPVLSSRVPEPRPGQCVND---------TETLPDSVLNFIRSHPLMDEAVAHR 210
TS W+ + S +P PRPG C+N+ + LPD L F++ PLMD+AV
Sbjct: 308 ETSFVKWV-MYSGELPVPRPGACINNAARTSGIKKSLNLPDKTLQFVKDKPLMDQAVHPI 366
Query: 211 DNKPVFYRRDLLFTHLVVDVV 231
KP+ +R LFT +VVD+V
Sbjct: 367 TGKPLLVKRGALFTRIVVDMV 387
>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 = 159 bits (404), Expect = 1e-44
Identities = 78/211 (36%), Positives = 107/211 (50%), Gaps = 14/211 (6%)
Query: 34 LQPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLK 93
L P G D ++FFF ETA EY + + RVARVC D GG+ L Q W T+LK
Sbjct: 182 LSPAEWGDEDGDDEIYFFFTETAREYDSYERIKVPRVARVCAGDLGGRKTLQQRWTTFLK 241
Query: 94 ARLNCSIPGEFPFYFNEIQDIYKVPGDD----TKFYGVFTTSTTGLMGSAICSFSIEDIE 149
A L C P E + +QD+ + FYG+F++ G SA+C+F +DI
Sbjct: 242 ADLLCPGP-EHGRASSILQDVTTLRPLPGAGTPIFYGIFSSQWEGASISAVCAFRPQDIR 300
Query: 150 RAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCV-NDTE--------TLPDSVLNFIRSH 200
R G F+E + LPV+ S VP+PRPG+C+ N+ + +LPD VL F+R H
Sbjct: 301 RVMNGPFREFKHDCNRGLPVMDSDVPQPRPGECITNNMKLLGFGSSLSLPDRVLTFVRDH 360
Query: 201 PLMDEAVAHRDNKPVFYRRDLLFTHLVVDVV 231
PLMD V D P+ D + + V
Sbjct: 361 PLMDRPVFPADGHPLLVTTDTAYLRVAAHRV 391
>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 = 159 bits (404), Expect = 2e-44
Identities = 90/246 (36%), Positives = 133/246 (54%), Gaps = 29/246 (11%)
Query: 36 PDFVGSYDIGKY-------VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNW 88
P F+ ++ I + ++FFFRE A++ + GK+ +R+ ++CK D GG L W
Sbjct: 199 PRFISAHLIPESDNPEDDKIYFFFRENAIDGEHTGKATHARIGQLCKNDFGGHRSLVNKW 258
Query: 89 ATYLKARLNCSIPGE--FPFYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSF 143
T+LKARL CS+PG +F+E+QD++ + D K Y VFTTS+ GSA+C +
Sbjct: 259 TTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYAVFTTSSNIFKGSAVCMY 318
Query: 144 SIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQC-------VNDTETLPDSVLNF 196
S+ DI R F+G + + W+P RVP PRPG C + T+ LPD V+ F
Sbjct: 319 SMTDIRRVFLGPYAHRDGPNYQWVPFQ-GRVPYPRPGTCPSKTFGGFDSTKDLPDDVITF 377
Query: 197 IRSHPLMDEAVAHRDNKPVFYRRDL--LFTHLVVDVVQYEVFGTTSEYIVYFAAT---TT 251
RSHP M V +N+P+ + D+ FT +VVD V+ E +Y V F T T
Sbjct: 378 ARSHPAMYNPVFPINNRPIIIKTDVDYQFTQIVVDRVEAE----DGQYDVMFIGTDMGTV 433
Query: 252 LRTVFV 257
L+ V +
Sbjct: 434 LKVVSI 439
>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 = 157 bits (399), Expect = 6e-44
Identities = 85/237 (35%), Positives = 121/237 (51%), Gaps = 27/237 (11%)
Query: 35 QPDFVGS--------YDIGK--YVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNIL 84
+P FVGS G ++FFF E AVEY + V +RVARVCK D GG L
Sbjct: 171 EPHFVGSAFVPESVGSFTGDDDKIYFFFSERAVEYDCDSEQVVARVARVCKGDLGGARTL 230
Query: 85 SQNWATYLKARLNCSIPGEFPFYFNEIQDIYKVPGD---DTKFYGVFTTSTTGLMGSAIC 141
+ W T+LKARL CSIP E+ YFN+++ ++ + G +T F+ VF + SA+C
Sbjct: 231 QKKWTTFLKARLLCSIP-EWQLYFNQLKAVFTLEGASWRNTTFFAVFQARWGDMDVSAVC 289
Query: 142 SFSIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTET---------LPDS 192
+ + +I++ F G +KE + W VP PRPG C+N+ LPD+
Sbjct: 290 EYQLGEIQQVFEGPYKEYSEQAQKWGRYTDP-VPSPRPGSCINNWHRDHGYTSSLELPDN 348
Query: 193 VLNFIRSHPLMDEAVAHRDNKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAAT 249
LNF++ HPLM++ V R +P+ + FTH+V V Y V F T
Sbjct: 349 TLNFVKKHPLMEDRVKPRLGRPLLVPCNSNFTHVVWTRVLG---LDGETYSVLFIGT 402
>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 = 157 bits (399), Expect = 7e-44
Identities = 84/218 (38%), Positives = 125/218 (57%), Gaps = 21/218 (9%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGEFPFY 107
++FFF E +VEY GK + R+ARVCK D GG L + W ++LKARL CSIP +
Sbjct: 201 IYFFFTEVSVEYEFVGKLLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSIP-DKNLV 259
Query: 108 FNEIQDIY--KVPG-DDTKFYGVFTTSTTGLMGSAICSFSIEDIERAFV-GKFKEQAT-- 161
FN + D++ K P + YGVFT + SA+C++++ +E F GK+ + AT
Sbjct: 260 FNVVNDVFILKSPTLKEPVIYGVFTPQLNNVGLSAVCAYNLSTVEEVFSKGKYMQSATVE 319
Query: 162 -STSAWLPVLSSRVPEPRPGQCVND---------TETLPDSVLNFIRSHPLMDEAVAHRD 211
S + W+ + VP+PRPG C+N+ + LPD L F++ HPLMD++V
Sbjct: 320 QSHTKWVR-YNGEVPKPRPGACINNEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIG 378
Query: 212 NKPVFYRRDLLFTHLVVDVVQYEVFGTTSEYIVYFAAT 249
N+P ++D+ +T +VVD VQ + GT Y V F +T
Sbjct: 379 NRPRLIKKDVNYTQIVVDRVQ-ALDGTI--YDVMFIST 413
>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 = 153 bits (388), Expect = 3e-42
Identities = 84/223 (37%), Positives = 121/223 (54%), Gaps = 28/223 (12%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGE--FP 105
++FFFRE ++E +V SR+ RVC D GG L W+T+LKARL CS+PG
Sbjct: 197 LYFFFREKSLEAPQ-SPAVLSRIGRVCLNDDGGHCCLVNKWSTFLKARLVCSVPGADGIE 255
Query: 106 FYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATS 162
+F+E++D++ P DTK Y VF+TS + GSA+C +S+ DI F G F +
Sbjct: 256 THFDELRDVFIQPTQDTKNPVIYAVFSTSGSVFKGSAVCVYSMADIRMVFNGPFAHKEGP 315
Query: 163 TSAWLPVLSSRVPEPRPGQC--------VNDTETLPDSVLNFIRSHPLMDEAVAHRDNKP 214
W+P + ++P PRPG C + T+ PD V+NF+R+HPLM AV +P
Sbjct: 316 NYQWMP-YTGKIPYPRPGTCPGGTFTPSMKSTKDYPDEVINFMRTHPLMYNAVYPVHRRP 374
Query: 215 VFYRRDL--LFTHLVVDVV-----QYEVF------GTTSEYIV 244
+ R ++ FT + VD V +YEV GT + IV
Sbjct: 375 LVVRTNVNYRFTTIAVDQVDAADGRYEVLFLGTDRGTVQKVIV 417
>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 = 148 bits (374), Expect = 2e-40
Identities = 84/237 (35%), Positives = 120/237 (50%), Gaps = 27/237 (11%)
Query: 35 QPDFVGSYDI-------GKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQN 87
+P FVGSY I V+FFF E A+E ++++RV RVC D GG+ +L
Sbjct: 176 EPKFVGSYMIPDNEDPDDNKVYFFFTEKALEAEGGNHAIYTRVGRVCANDQGGQRMLVNK 235
Query: 88 WATYLKARLNCSIPGE--FPFYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICS 142
W+T+LK RL CS+PG +F+E++D++ + D K +G+F+T++ G AIC
Sbjct: 236 WSTFLKTRLICSVPGPNGIDTHFDELEDVFLLRTRDNKNPEIFGLFSTTSNIFKGYAICV 295
Query: 143 FSIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQC---VN-----DTETLPDSVL 194
+ + I AF G F + W V +VP PRPG C VN T+ PD L
Sbjct: 296 YHMASIRAAFNGPFAHKEGPEYHW-SVYEGKVPYPRPGSCASKVNGGHYGTTKDYPDEAL 354
Query: 195 NFIRSHPLMDEAVAHRDNKPVFYRRD--LLFTHLVVDVVQYEVFGTTSEYIVYFAAT 249
F RSHPLM +AV +P+ + D + VD V+ E +Y V F T
Sbjct: 355 RFARSHPLMYQAVKPVHKRPILVKTDGKYNLKQIAVDRVEAE----DGQYDVLFIGT 407
>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 = 138 bits (350), Expect = 7e-37
Identities = 87/270 (32%), Positives = 127/270 (47%), Gaps = 36/270 (13%)
Query: 3 ISRT--HRS-LYVASDERIKQIALVMCAHRY-DNCLQPDFVGSYDIGKYVFFFFRETAVE 58
I R RS L +D+R+ + AH DN + + V+FFF E A E
Sbjct: 154 IFRGFGTRSPLRTETDQRLLHEPRFVAAHLIPDNADRDN--------DKVYFFFTERATE 205
Query: 59 Y-INCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGE--FPFYFNEIQDIY 115
+ ++ SRV R+C D GG+ +L W+T++KARL CS+PG +F++++D++
Sbjct: 206 TAEDDDGAIHSRVGRLCANDAGGQRVLVNKWSTFIKARLVCSVPGPHGIQTHFDQLEDVF 265
Query: 116 KVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATSTSAWLPVLSS 172
+ D K Y +F+T + G A+C +S+ DI F G F + W P
Sbjct: 266 LLRTKDGKSPEIYALFSTISNVFQGFAVCVYSMADIWEVFNGPFAHKDGPDHQWGP-YEG 324
Query: 173 RVPEPRPGQC-----------VNDTETLPDSVLNFIRSHPLMDEAVAHRDNKPVFYRRDL 221
+VP PRPG C T+ PD VL F R+HPLM V +PV + L
Sbjct: 325 KVPYPRPGVCPSKITAQPGRAFRSTKDYPDEVLQFARAHPLMWRPVYPSHRRPVLVKTGL 384
Query: 222 LF--THLVVDVVQYEVFGTTSEYIVYFAAT 249
+ T +VVD V+ E Y V F T
Sbjct: 385 PYRLTQIVVDRVEAE----DGYYDVMFIGT 410
>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 = 134 bits (339), Expect = 2e-35
Identities = 68/199 (34%), Positives = 105/199 (52%), Gaps = 16/199 (8%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARLNCSIPGE--FP 105
++FF +E + K + S +ARVC DTGG+ L W T+LKARL CS+ E
Sbjct: 196 LYFFLKERLTDNSGSTKQIHSMIARVCPNDTGGQRSLVNKWTTFLKARLVCSVMDEDGTE 255
Query: 106 FYFNEIQDIYKVPGDDTK---FYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATS 162
+F+E++D++ + D+ + YG+FTTS++ GSA+C + + DI+ F G F +
Sbjct: 256 THFDELEDVFLLETDNPRTTLVYGIFTTSSSVFKGSAVCVYHMSDIQTVFNGPFAHKEGP 315
Query: 163 TSAWLPVLSSRVPEPRPGQC--------VNDTETLPDSVLNFIRSHPLMDEAVAHRDNKP 214
+ R+P PRPG C + T+ PD V+ FIR+HPLM + +P
Sbjct: 316 NHQLIA-YQGRIPYPRPGTCPGGAFTPNMQSTKEFPDDVVTFIRNHPLMFNPIYPIGRRP 374
Query: 215 VFYR--RDLLFTHLVVDVV 231
+ R D +T + VD V
Sbjct: 375 LLVRTGTDYKYTKIAVDRV 393
>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 = 121 bits (304), Expect = 8e-31
Identities = 70/191 (36%), Positives = 103/191 (53%), Gaps = 21/191 (10%)
Query: 48 VFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILS-QNWATYLKARLNCSIPGEFPF 106
+++FFRE + + SRVAR+CK D GG + LS W+T+LKARL C P P
Sbjct: 169 IYYFFREDNEDKGPEAEPNISRVARLCKEDQGGTSSLSTSKWSTFLKARLVCGDPAT-PM 227
Query: 107 YFNEIQDIYKVPGD---DTKFYGVFTTSTTGLMGSAICSFSIEDIERAFVGKFKEQATST 163
FN +QD++ +P + + YGVF+ +T G SA+CS+S+ DI++ F T
Sbjct: 228 NFNRLQDVFLLPKEEWREAVVYGVFS-NTWG--SSAVCSYSLGDIDKVF---------RT 275
Query: 164 SAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAV--AHRDNKPVFYRRDL 221
S+ L S +P PRPG CV +T P +F HP +D+ + PVF +D
Sbjct: 276 SS-LKGYSGSLPNPRPGTCVPPEQTHPSETFSFADEHPELDDRIEPDEPRKLPVFQNKD- 333
Query: 222 LFTHLVVDVVQ 232
+ +VVD V+
Sbjct: 334 HYQKVVVDEVR 344
>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 = 88.8 bits (220), Expect = 1e-19
Identities = 42/123 (34%), Positives = 62/123 (50%), Gaps = 6/123 (4%)
Query: 35 QPDFVGSYDIGK---YVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATY 91
+ FV ++ G V+FFFR+ VEY+ G R+ARVCK D GG + L + ++
Sbjct: 169 EITFVYAFVSGDDDDEVYFFFRQEPVEYLKKGMVYVPRIARVCKLDVGGCHRLKKKLTSF 228
Query: 92 LKARLNCSIPGEFPFYFNEIQDIY--KVPGDDTKFYGVFTTSTTGLMGSAICSFSIEDIE 149
LKA LNCS P F FN +QD + +F++ + SA+C++ DI
Sbjct: 229 LKADLNCSRPQS-GFAFNLLQDATGDTKNLIQDVKFAIFSSCLNKSVESAVCAYLFTDIN 287
Query: 150 RAF 152
F
Sbjct: 288 NVF 290
>gnl|CDD|143180 cd04979, Ig_Semaphorin_C, Immunoglobulin (Ig)-like domain of
semaphorin. Ig_Semaphorin_C; Immunoglobulin (Ig)-like
domain in semaphorins. Semaphorins are transmembrane
protein that have important roles in a variety of
tissues. Functionally, semaphorins were initially
characterized for their importance in the development of
the nervous system and in axonal guidance. Later they
have been found to be important for the formation and
functioning of the cardiovascular, endocrine,
gastrointestinal, hepatic, immune, musculoskeletal,
renal, reproductive, and respiratory systems.
Semaphorins function through binding to their receptors
and transmembrane semaphorins also serves as receptors
themselves. Although molecular mechanism of semaphorins
is poorly understood, the Ig-like domains may involve in
ligand binding or dimerization.
Length = 89
Score = 50.9 bits (122), Expect = 2e-08
Identities = 25/94 (26%), Positives = 35/94 (37%), Gaps = 13/94 (13%)
Query: 280 LKQTVTWGQSVHLSCFVKLP-ASMANQPMSWYHYSKDKGRYQIKFRSDKFIRTVDGGLVI 338
TV G SV L C K AS+ W R + ++ + + GL+I
Sbjct: 4 KVVTVVEGNSVFLECSPKSNLASVV-----WLFQGGPLQRKEE---PEERLLVTEDGLLI 55
Query: 339 MAVEELDAGKYDCWLG----NTVLCTHNLTVDAH 368
+V DAG Y C L T++L V
Sbjct: 56 RSVSPADAGVYTCQSVEHGFKQTLATYSLNVLEV 89
>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 = 47.5 bits (113), Expect = 7e-06
Identities = 39/211 (18%), Positives = 68/211 (32%), Gaps = 35/211 (16%)
Query: 37 DFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARL 96
F +++ YV+F F + + + +AR+C+ D ++ +Y + L
Sbjct: 191 QFRYAFEDNNYVYFLFNQQ----LGHPDKNRTLIARLCEND--------HHYYSYTEMDL 238
Query: 97 NCSIPGEFPFYFNEIQDIY-----KVPG--------DDTKFYGVFTTSTTGLMGSAICSF 143
NC +N+ Q Y K D + VF+ SA+C F
Sbjct: 239 NCRDGAN---AYNKCQAAYVSTPGKELAQNYGNSILSDKVLFAVFSRDEKDSGESALCMF 295
Query: 144 SIEDIERAFVGKFKEQATSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLM 203
++ I + T T V + C + + +F +
Sbjct: 296 PLKSINAKMEANREACYTGTIDDRDVFYKPFHSQKDIICGSHQ---QKNSKSFPCGSEHL 352
Query: 204 DEAVAHRDN----KPVFYRRDLLFTHLVVDV 230
+ RD PV R L T + V V
Sbjct: 353 PYPLGSRDELALTAPVLQRGGLNLTAVTVAV 383
>gnl|CDD|200506 cd11245, Sema_plexin_B, The Sema domain, a protein interacting
module, of Plexin B. Plexins, which contain semaphorin
domains, function as receptors of semaphorins and may be
the ancestors of semaphorins. There are three members of
the Plexin B subfamily, namely B1, B2 and B3. Plexins
B1, B2 and B3 are receptors for Sema4D, Sema4C and
Sema4G, and Sema5A, respectively. The activation of
plexin B1 by Sema4D produces an acute collapse of axonal
growth cones in hippocampal and retinal neurons over the
early stages of neurite outgrowth and promotes branching
and complexity. By signaling the effect of Sema4C and
Sema4G, the plexin B2 receptor is critically involved in
neural tube closure and cerebellar granule cell
development. Plexin B3, the receptor of Sema5A, 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. Small GTPases play important roles in plexin B
signaling. Plexin B1 activates Rho through Rho-specific
guanine nucleotide exchange factors, leading to neurite
retraction. Plexin B1 possesses an intrinsic
GTPase-activating protein activity for R-Ras and induces
growth cone collapse through R-Ras inactivation. 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 = 440
Score = 46.5 bits (110), Expect = 1e-05
Identities = 30/134 (22%), Positives = 58/134 (43%), Gaps = 25/134 (18%)
Query: 27 AHRYDNCLQPDFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQ 86
A RY + DFV ++ Y++F F + + ++R+C+ D
Sbjct: 179 ASRYHH----DFVYAFADNGYIYFLFSRRPGT---ADSTKRTYISRLCEND--------H 223
Query: 87 NWATYLKARLNCSIPGEFPFYFNEIQDIYKVPG----DDTKFYGVFTT---STTGLMG-S 138
++ +Y++ LNC++ E +N +Q Y + +GVF+ ST G S
Sbjct: 224 HYYSYVELPLNCTVNQEN--TYNLVQAAYLAKPGKVLNGKVLFGVFSADEASTAAPDGRS 281
Query: 139 AICSFSIEDIERAF 152
A+C + + ++ F
Sbjct: 282 ALCMYPLSSVDARF 295
>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 = 41.9 bits (99), Expect = 3e-04
Identities = 33/132 (25%), Positives = 54/132 (40%), Gaps = 28/132 (21%)
Query: 37 DFVGSYDIGKYVFFFFRETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLKARL 96
+V + G + +F + + ++ SR+ RVC+ D N+ +Y + L
Sbjct: 184 KYVYGFSSGGFSYFVTVQR--KSVDDESPYISRLVRVCQSD--------SNYYSYTEVPL 233
Query: 97 NCSIPGEFPFYFNEIQDIYKVP------------GDDTKFYGVFTTSTTG----LMGSAI 140
C+ G +N +Q Y DD +GVF+ S SA+
Sbjct: 234 QCT--GGDGTNYNLLQAAYVGKAGSDLARSLGISTDDDVLFGVFSKSKGPSAEPSSKSAL 291
Query: 141 CSFSIEDIERAF 152
C FS++DIE AF
Sbjct: 292 CVFSMKDIEAAF 303
>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 = 40.2 bits (94), Expect = 0.001
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 30/122 (24%)
Query: 38 FVGSYDIGKYVFFFFR----ETAVEYINCGKSVFSRVARVCKRDTGGKNILSQNWATYLK 93
+VG++ YV+F FR EY + VARVC DT N +Y++
Sbjct: 188 YVGAFAHNGYVYFLFRRRGARAQAEY-------RTYVARVCLGDT--------NLYSYVE 232
Query: 94 ARLNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTS----TTGLMGSAICSFSIEDIE 149
L C +N Q Y PG T F VF T +A+C++ + +++
Sbjct: 233 VPLVCQGG------YNLAQAAYLAPGQGTLF-VVFAAGQGSTPTPTDQTALCAYPLVELD 285
Query: 150 RA 151
A
Sbjct: 286 SA 287
>gnl|CDD|214653 smart00410, IG_like, Immunoglobulin like. IG domains that cannot
be classified into one of IGv1, IGc1, IGc2, IG.
Length = 85
Score = 33.2 bits (76), Expect = 0.035
Identities = 21/86 (24%), Positives = 28/86 (32%), Gaps = 16/86 (18%)
Query: 287 GQSVHLSCFVKLPASMANQPMSWYHYSKD----KGRYQIKFRSDKFIRTVDGGLVIMAVE 342
G+SV LSC ++WY GR+ + L I V
Sbjct: 9 GESVTLSCEAS---GSPPPEVTWYKQGGKLLAESGRFSVSRSGSTST------LTISNVT 59
Query: 343 ELDAGKYDCWLGNT---VLCTHNLTV 365
D+G Y C N+ LTV
Sbjct: 60 PEDSGTYTCAATNSSGSASSGTTLTV 85
>gnl|CDD|214652 smart00409, IG, Immunoglobulin.
Length = 85
Score = 33.2 bits (76), Expect = 0.035
Identities = 21/86 (24%), Positives = 28/86 (32%), Gaps = 16/86 (18%)
Query: 287 GQSVHLSCFVKLPASMANQPMSWYHYSKD----KGRYQIKFRSDKFIRTVDGGLVIMAVE 342
G+SV LSC ++WY GR+ + L I V
Sbjct: 9 GESVTLSCEAS---GSPPPEVTWYKQGGKLLAESGRFSVSRSGSTST------LTISNVT 59
Query: 343 ELDAGKYDCWLGNT---VLCTHNLTV 365
D+G Y C N+ LTV
Sbjct: 60 PEDSGTYTCAATNSSGSASSGTTLTV 85
>gnl|CDD|143165 cd00096, Ig, Immunoglobulin domain. Ig: immunoglobulin (Ig) domain
found in the Ig superfamily. The Ig superfamily is a
heterogenous group of proteins, built on a common fold
comprised of a sandwich of two beta sheets. Members of
this group are components of immunoglobulin, neuroglia,
cell surface glycoproteins, such as, T-cell receptors,
CD2, CD4, CD8, and membrane glycoproteins, such as,
butyrophilin and chondroitin sulfate proteoglycan core
protein. A predominant feature of most Ig domains is a
disulfide bridge connecting the two beta-sheets with a
tryptophan residue packed against the disulfide bond.
Length = 74
Score = 30.5 bits (68), Expect = 0.21
Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 290 VHLSCFVKLPASMANQPMSWYHYSKDKG-RYQIKFRSDKFIRTVDGGLVIMAVEELDAGK 348
V L+C P ++W K + RS + + L I V D+G
Sbjct: 1 VTLTCLASGPPPPT---ITWLKNGKPLPSSVLTRVRSSRGTSSGSSTLTISNVTLEDSGT 57
Query: 349 YDCWLGN 355
Y C N
Sbjct: 58 YTCVASN 64
>gnl|CDD|143281 cd05873, Ig_Sema4D_like, Immunoglobulin (Ig)-like domain of the
class IV semaphorin Sema4D. Ig_Sema4D_like;
Immunoglobulin (Ig)-like domain of Sema4D. Sema4D is a
Class IV semaphorin. Semaphorins are classified based on
structural features additional to the Sema domain.
Sema4D has extracellular Sema and Ig domains, a
transmembrane domain, and a short cytoplasmic domain.
Sema4D plays a part in the development of GABAergic
synapses. Sema4D in addition is an immune semaphorin. It
is abundant on resting T cells; its expression is weak
on resting B cells and antigen presenting cells (APCs),
but is upregulated by various stimuli. The receptor used
by Sema4D in the immune system is CD72. Sem4D enhances
the activation of B cells and DCs through binding CD72,
perhaps by reducing CD72s inhibitory signals. The
receptor used by Sema4D in the non-lymphatic tissues is
plexin-B1. Sem4D is anchored to the cell surface but its
extracellular domain can be released from the cell
surface by a metalloprotease-dependent process. Sem4D
may mediate its effects in its membrane bound form,
and/or its cleaved form.
Length = 87
Score = 30.6 bits (69), Expect = 0.32
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 280 LKQTVTWGQSVHLSCFVKLPASMANQPMSWYHYSKDKGRYQIKFRSDKFIRTVDGGLVIM 339
++T G + L C +++A + W K + S K+ GL+I
Sbjct: 4 RQRTFKLGNNAELKC--SPKSNLAR--VVWKFDGK-----VLTPESAKY-LLYRDGLLIF 53
Query: 340 AVEELDAGKYDC 351
E DAG+Y C
Sbjct: 54 NASEADAGRYQC 65
>gnl|CDD|184358 PRK13874, PRK13874, conjugal transfer protein TrbJ; Provisional.
Length = 230
Score = 31.8 bits (73), Expect = 0.44
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 132 TTGLMGSA--ICSFSIEDIERAFVGKFKEQATSTS 164
T L+ A I ++ ++ I+RAF + E + + S
Sbjct: 88 TQQLLAQAQGI-AYDVQSIDRAFQRLYPEASATVS 121
>gnl|CDD|143201 cd05724, Ig2_Robo, Second immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Ig2_Robo: domain similar to the
second immunoglobulin (Ig)-like domain in Robo
(roundabout) receptors. Robo receptors play a role in
the development of the central nervous system (CNS), and
are receptors of Slit protein. Slit is a repellant
secreted by the neural cells in the midline. Slit acts
through Robo to prevent most neurons from crossing the
midline from either side. Three mammalian Robo homologs
(robo1, -2, and -3), and three mammalian Slit homologs
(Slit-1,-2, -3), have been identified. Commissural
axons, which cross the midline, express low levels of
Robo; longitudinal axons, which avoid the midline,
express high levels of Robo. robo1, -2, and -3 are
expressed by commissural neurons in the vertebrate
spinal cord and Slits 1, -2, -3 are expressed at the
ventral midline. Robo-3 is a divergent member of the
Robo family which instead of being a positive regulator
of slit responsiveness, antagonizes slit responsiveness
in precrossing axons. The Slit-Robo interaction is
mediated by the second leucine-rich repeat (LRR) domain
of Slit and the two N-terminal Ig domains of Robo, Ig1
and Ig2. The primary Robo binding site for Slit2 has
been shown by surface plasmon resonance experiments and
mutational analysis to be is the Ig1 domain, while the
Ig2 domain has been proposed to harbor a weak secondary
binding site.
Length = 86
Score = 29.7 bits (67), Expect = 0.53
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 325 SDKFIRTVDGG-LVIMAVEELDAGKYDCWLGNTV 357
++ +R VD G L+I + D G Y C N V
Sbjct: 41 DNERVRIVDDGNLLIAEARKSDEGTYKCVATNMV 74
>gnl|CDD|143223 cd05746, Ig4_Peroxidasin, Fourth immunoglobulin (Ig)-like domain of
peroxidasin. Ig4_Peroxidasin: the fourth immunoglobulin
(Ig)-like domain in peroxidasin. Peroxidasin has a
peroxidase domain and interacting extracellular motifs
containing four Ig-like domains. It has been suggested
that peroxidasin is secreted, and has functions related
to the stabilization of the extracellular matrix. It may
play a part in various other important processes such as
removal and destruction of cells, which have undergone
programmed cell death, and protection of the organism
against non-self.
Length = 69
Score = 28.7 bits (64), Expect = 0.89
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 296 VKLPASMANQPMSWYHYSKDKGRYQIKFRSDKFIRTVDGGLVIMAVEELDAGKYDCWLGN 355
V++P S P ++KD Q+ S KF + +G L I V D G+Y+C N
Sbjct: 1 VQIPCSAQGDPEPTITWNKDG--VQVT-ESGKFHISPEGYLAIRDVGVADQGRYECVARN 57
Query: 356 TV 357
T+
Sbjct: 58 TI 59
>gnl|CDD|219665 pfam07959, Fucokinase, L-fucokinase. In the salvage pathway of
GDP-L-fucose, free cytosolic fucose is phosphorylated by
L-fucokinase to form L-fucose-L-phosphate, which is then
further converted to GDP-L-fucose in the reaction
catalyzed by GDP-L-fucose pyrophosphorylase.
Length = 414
Score = 31.0 bits (70), Expect = 1.1
Identities = 32/160 (20%), Positives = 47/160 (29%), Gaps = 42/160 (26%)
Query: 165 AWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRS---HPLMDEAVAHRDNKPVFYRRDL 221
A P + P +S L +R H L + V D
Sbjct: 190 ALGPGATREHPRLT------SRVMKEESYLKLMRQKIFHLLKGTPLN------VVVLPDG 237
Query: 222 LFTHLVVDVVQYEVFGTTSEYIVYFAATTTLRTVFVKVRLLQDVSNTSDSICESSVGRLK 281
F H FGT++EY+ + + + L V VR + +
Sbjct: 238 GFYH----------FGTSAEYLDHLTSDSGLG---VGVRHFSSSPAITPQDIAA------ 278
Query: 282 QTVTWGQSVHLSCFVKLPASMANQPMSWYHYSKDKGRYQI 321
SV LS + S+ P S YS G +I
Sbjct: 279 ------TSVILSSLLDSGVSVG--PGSVVEYSHLGGPVRI 310
>gnl|CDD|197706 smart00408, IGc2, Immunoglobulin C-2 Type.
Length = 63
Score = 28.1 bits (63), Expect = 1.2
Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 10/65 (15%)
Query: 287 GQSVHLSCFVKLPASMANQPMSWYHYSKDKGRYQIKFRSDKFIRTVDGGLVIMAVEELDA 346
GQSV L+C + + N ++W K L I +V D+
Sbjct: 2 GQSVTLTCPAE-GNPVPN--ITWLKDGK-------PLPESNRFVASGSTLTIKSVSLEDS 51
Query: 347 GKYDC 351
G Y C
Sbjct: 52 GLYTC 56
>gnl|CDD|143167 cd00099, IgV, Immunoglobulin variable domain (IgV). IgV:
Immunoglobulin variable domain (IgV). Members of the IgV
family are components of immunoglobulin (Ig) and T cell
receptors. The basic structure of Ig molecules is a
tetramer of two light chains and two heavy chains linked
by disulfide bonds. In Ig, each chain is composed of one
variable domain (IgV) and one or more constant domains
(IgC); these names reflect the fact that the variability
in sequences is higher in the variable domain than in
the constant domain. Within the variable domain, there
are regions of even more variability called the
hypervariable or complementarity-determining regions
(CDRs) which are responsible for antigen binding. A
predominant feature of most Ig domains is the disulfide
bridge connecting 2 beta-sheets with a tryptophan
residue packed against the disulfide bond.
Length = 105
Score = 28.8 bits (65), Expect = 1.8
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 20/86 (23%)
Query: 283 TVTWGQSVHLSCFVKLPASMANQPMSWY------------HYSKDKGRYQIKFRSDKFIR 330
+V+ G+SV LSC S + WY + S + +Y +F
Sbjct: 2 SVSEGESVTLSCTYSGSFSSYY--IFWYRQKPGKGPELLIYISSNGSQYAGGV-KGRFSG 58
Query: 331 TVDGG-----LVIMAVEELDAGKYDC 351
T D L I +++ D+ Y C
Sbjct: 59 TRDSSKSSFTLTISSLQPEDSAVYYC 84
>gnl|CDD|143330 cd07706, IgV_TCR_delta, Immunoglobulin (Ig) variable (V) domain of
T-cell receptor (TCR) delta chain. IgV_TCR_delta:
immunoglobulin (Ig) variable (V) domain of the delta
chain of gamma/delta T-cell receptors (TCRs). TCRs
mediate antigen recognition by T lymphocytes, and are
heterodimers consisting of alpha and beta chains or
gamma and delta chains. Each chain contains a variable
(V) and a constant (C) region. The majority of T cells
contain alpha/beta TCRs but a small subset contain
gamma/delta TCRs. Alpha/beta TCRs recognize antigen as
peptide fragments presented by major histocompatibility
complex (MHC) molecules. Gamma/delta TCRs recognize
intact protein antigens; they recognize protein antigens
directly and without antigen processing, and MHC
independently of the bound peptide. Gamma/delta T cells
can also be stimulated by non-peptide antigens such as
small phosphate- or amine-containing compounds. The
variable domain of gamma/delta TCRs is responsible for
antigen recognition and is located at the N-terminus of
the receptor.
Length = 116
Score = 28.6 bits (64), Expect = 2.4
Identities = 25/91 (27%), Positives = 36/91 (39%), Gaps = 25/91 (27%)
Query: 282 QTVTWGQSVHLSCFVKLPASMANQPMSWY-------------HYSKD----KGRYQIKF- 323
+V G+ V L+C + S N + WY S KGRY + F
Sbjct: 9 VSVQVGEEVTLNCRYE--TSWTNYYIFWYKQLPSGEMTFLIRQKSIYGNATKGRYSVNFQ 66
Query: 324 RSDKFIRTVDGGLVIMAVEELDAGKYDCWLG 354
++ K I L I A++ D+ KY C L
Sbjct: 67 KAQKSI-----SLTISALQLEDSAKYFCALS 92
>gnl|CDD|219514 pfam07686, V-set, Immunoglobulin V-set domain. This domain is
found in antibodies as well as neural protein P0 and
CTL4 amongst others.
Length = 114
Score = 28.0 bits (62), Expect = 3.5
Identities = 17/83 (20%), Positives = 23/83 (27%), Gaps = 20/83 (24%)
Query: 287 GQSVHLSCFVKLPASMANQPMSWYHYSKDKGRYQI------------------KFRSDKF 328
G SV L C + + + WY KG I +
Sbjct: 16 GGSVTLPCSFSSSSGSTS--VYWYKQPLGKGPELIIHYVTSTPNGKVGPRFKGRVTLSGN 73
Query: 329 IRTVDGGLVIMAVEELDAGKYDC 351
D L I + D+G Y C
Sbjct: 74 GSKNDFSLTISNLRLSDSGTYTC 96
>gnl|CDD|223407 COG0330, HflC, Membrane protease subunits, stomatin/prohibitin
homologs [Posttranslational modification, protein
turnover, chaperones].
Length = 291
Score = 29.3 bits (66), Expect = 3.5
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 17/91 (18%)
Query: 205 EAVAHRDNKPV------FYRRDLLFTHLVVDVVQYEVFGTT-SEYIVYFAATTTLRTVFV 257
+ V +DN V YR V D + V+ +E + + LR+V
Sbjct: 77 QEVITKDNVIVSVDAVVQYR--------VTDPQKA-VYNVENAEAALRQLVQSALRSVIG 127
Query: 258 KVRLLQDVSNTSDSICESSVGRLKQTVT-WG 287
++ L + ++ I L + WG
Sbjct: 128 RMTLDELLTERRAEINAKIREILDEAADPWG 158
>gnl|CDD|216016 pfam00602, Flu_PB1, Influenza RNA-dependent RNA polymerase subunit
PB1. Two GTP binding sites exist in this protein.
Length = 740
Score = 29.1 bits (65), Expect = 4.3
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 11/73 (15%)
Query: 80 GKNILSQNWATYLKARLNCSIPGEFPFYFNE-----IQDIYKVPGDDT------KFYGVF 128
GK I+ ++ + + GE P FNE I+ + + D T G+F
Sbjct: 353 GKGIMLKSKTKRKEVVIKAEALGEIPDAFNEETRNLIKKLEPMIEDGTIRLSPGMLMGMF 412
Query: 129 TTSTTGLMGSAIC 141
+T L S++
Sbjct: 413 NMLSTVLGVSSLS 425
>gnl|CDD|234248 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein family
are HemK (PrmC), a protein once thought to be involved
in heme biosynthesis but now recognized to be a
protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3 [Protein fate, Protein modification
and repair].
Length = 251
Score = 28.6 bits (65), Expect = 4.8
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 170 LSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPL 202
+S V PRP +TE L ++ L ++ PL
Sbjct: 62 VSPGVLIPRP-----ETEELVEAALERLKKGPL 89
>gnl|CDD|224992 COG2081, COG2081, Predicted flavoproteins [General function
prediction only].
Length = 408
Score = 28.7 bits (65), Expect = 5.4
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 162 STSAWLPVLSSR---VPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHRDNKPVFYR 218
ST P+ + RP TL +S L + L ++ K + ++
Sbjct: 173 STGFGYPIARQFGHTITPLRPALV---PFTLDESFLERLAGLSLKSVPLSVTAGKGITFQ 229
Query: 219 RDLLFTH 225
DLLFTH
Sbjct: 230 GDLLFTH 236
>gnl|CDD|200469 cd11330, AmyAc_OligoGlu, Alpha amylase catalytic domain found in
oligo-1,6-glucosidase (also called isomaltase;
sucrase-isomaltase; alpha-limit dextrinase) and related
proteins. Oligo-1,6-glucosidase (EC 3.2.1.10)
hydrolyzes the alpha-1,6-glucosidic linkage of
isomalto-oligosaccharides, pannose, and dextran. Unlike
alpha-1,4-glucosidases (EC 3.2.1.20), it fails to
hydrolyze the alpha-1,4-glucosidic bonds of
maltosaccharides. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 472
Score = 28.8 bits (65), Expect = 5.7
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 161 TSTSAWLPVLSSRVPEPRPGQCVNDTETLPDSVLNFIRSHPLMDEAVAHRDNKPVFYRRD 220
++ WLPV P V+ E P SVLNF R +A R +P
Sbjct: 413 STAKPWLPV-----PPEHLALAVDVQEKDPGSVLNFYR------RFLAWRKAQPALRTGT 461
Query: 221 LLF 223
+ F
Sbjct: 462 ITF 464
>gnl|CDD|223246 COG0168, TrkG, Trk-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 499
Score = 28.4 bits (64), Expect = 6.6
Identities = 15/50 (30%), Positives = 16/50 (32%), Gaps = 5/50 (10%)
Query: 96 LNCSIPGEFPFYFNEIQDIYKVPGDDTKFYGVFTTSTTGLMGSAICSFSI 145
L S G PF + D GV TT T L G SI
Sbjct: 75 LVASSFGALPFTASSSTDAL-----FEGLSGVTTTGATVLFGLDSLPQSI 119
>gnl|CDD|203928 pfam08390, TRAM1, TRAM1-like protein. This family comprises
sequences that are similar to human TRAM1. This is a
transmembrane protein of the endoplasmic reticulum,
thought to be involved in the membrane transfer of
secretory proteins. The region featured in this family
is found N-terminal to the longevity-assurance protein
region (pfam03798).
Length = 65
Score = 26.0 bits (58), Expect = 6.9
Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 16/55 (29%)
Query: 30 YDNCLQPDFVGSYDIGK----YVFF------FFRETAVEYINCGKSVFSRVARVC 74
Y+ P G Y G +VFF F R +EY V +AR
Sbjct: 10 YNVTTTPPGTGLYGKGIKDLYFVFFYVIFFTFLRAFIMEY------VLRPLARKL 58
>gnl|CDD|191810 pfam07679, I-set, Immunoglobulin I-set domain.
Length = 90
Score = 26.8 bits (60), Expect = 7.1
Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 20/77 (25%)
Query: 282 QTVTWGQSVHLSCFVKLPASMANQPM--SWYHYSKDK-----GRYQIKFRSDKFIRTVDG 334
V G+S +C V + SW+ + R+++ +
Sbjct: 10 VEVQEGESARFTCTVT-----GDPDPTVSWFK--DGQPLRSSDRFKVTYEGG------TY 56
Query: 335 GLVIMAVEELDAGKYDC 351
L I V+ D GKY C
Sbjct: 57 TLTISNVQPDDEGKYTC 73
>gnl|CDD|215677 pfam00047, ig, Immunoglobulin domain. Members of the
immunoglobulin superfamily are found in hundreds of
proteins of different functions. Examples include
antibodies, the giant muscle kinase titin and receptor
tyrosine kinases. Immunoglobulin-like domains may be
involved in protein-protein and protein-ligand
interactions. The Pfam alignments do not include the
first and last strand of the immunoglobulin-like domain.
Length = 62
Score = 25.6 bits (56), Expect = 9.8
Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 7/68 (10%)
Query: 287 GQSVHLSCFVKLPASMANQPMSWYHYSKDKGRYQIKFRSDKF-IRTVDGGLVIMAVEELD 345
G SV L+C V P ++W+ K+ + R L I V D
Sbjct: 1 GSSVTLTCSVSGPPQ---VDVTWF---KEGKGLEESTTVGTDENRVSSITLTISNVTPED 54
Query: 346 AGKYDCWL 353
+G Y C +
Sbjct: 55 SGTYTCVV 62
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
0.323 0.136 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: 19,020,827
Number of extensions: 1785998
Number of successful extensions: 1390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1273
Number of HSP's successfully gapped: 64
Length of query: 378
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 279
Effective length of database: 6,546,556
Effective search space: 1826489124
Effective search space used: 1826489124
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (26.9 bits)