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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVS 61
Cdd:cd11240   396 LFLGTEDGFLHKAVSLDGGMHIIEEIQLFDQPQPVKNLLLSSSKGVLYVGSSSGVVQVPLS 456

Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas some members show 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1561713857  63 CHQYKYCLDCILARDPYCAWSQSAKECLLLSNPTGHTREQ 102
Cdd:pfam01437   2 CSQYTSCSSCLAARDPYCGWCSSEGRCVRRSACGAPEGNC 41

WH1 domain; WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homolog. A subset of WH1 domains has been termed a "EVH1" domain and appear to bind a polyproline motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 102 QPIFSTRAHVFQIDPATKRNWIPAsKHALTVSYFYDATRNVYRIISVG--GTKAIINSTITPNMTFTKTSQKFGQWADSR 179
Cdd:pfam00568   9 QTICTAVAQVYLADPDNKRHWIKA-KHSGVVCFVKDSPQNSYFIRLVDiqDGKVIWNQEIYPNMEYNQARPFFHTFADSR 87

                          90       100
                  ....*....|....*....|....*.
gi 1561713857 180 AntVYGLGFASEQHLSQFAEKFQEVK 205
Cdd:pfam00568  88 C--VYGLNFASEEEATKFAKAVQEAL 111

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVS 61
Cdd:cd11240   396 LFLGTEDGFLHKAVSLDGGMHIIEEIQLFDQPQPVKNLLLSSSKGVLYVGSSSGVVQVPLS 456

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  251 RSQSADVEIT---TEKERLKKMLSEGSVSEVQWEAEFFSLQDNNNKLVAALHEANANVDQWKKQLAAYQEETEMLRQRVA 327
Cdd:TIGR02169  323 RLAKLEAEIDkllAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREIN 402

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  328 ELESQgahDSSSENNKEELSQTLEELELLIKAKDEEIQMLKSQKCGR----WEAEGEREETLQKL----QELEARNAE-- 397
Cdd:TIGR02169  403 ELKRE---LDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKaleiKKQEWKLEQLAADLskyeQELYDLKEEyd 479

                          170       180
                   ....*....|....*....|....*..
gi 1561713857  398 -LERRLHLAEQTLAETLAEREKIQNEV 423
Cdd:TIGR02169  480 rVEKELSKLQRELAEAEAQARASEERV 506

Plexin repeat; A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas some members show 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1561713857  63 CHQYKYCLDCILARDPYCAWSQSAKECLLLSNPTGHTREQ 102
Cdd:pfam01437   2 CSQYTSCSSCLAARDPYCGWCSSEGRCVRRSACGAPEGNC 41

Coiled-coil domain-containing protein 158; CCDC158 is a family of proteins found in eukaryotes. The function is not known.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  262 EKERLKKMLsEGSVSEVQWEAEffslqdnnnKLVAALHEANANVDQWKKQLAAYQEETEMLRQRVAELESQGAHDSSSEN 341
Cdd:pfam15921  427 EVQRLEALL-KAMKSECQGQME---------RQMAAIQGKNESLEKVSSLTAQLESTKEMLRKVVEELTAKKMTLESSER 496

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  342 NKEELSQTLEELELLIKAKDEEIQMLKSQKcgrweaegerEETLQKLQELEA-----RNAELE---RRLHLAEQ-TLAET 412
Cdd:pfam15921  497 TVSDLTASLQEKERAIEATNAEITKLRSRV----------DLKLQELQHLKNegdhlRNVQTEceaLKLQMAEKdKVIEI 566

                          170
                   ....*....|....*.
gi 1561713857  413 LaeREKIQNEVTKVAE 428
Cdd:pfam15921  567 L--RQQIENMTQLVGQ 580

semaphorin domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1561713857    1 MFLGTDDGYLHKAFNCDGG----MFVVEELQLFLSPEPVR 36
Cdd:smart00630 351 LFLGTSDGRILKVVLSESSssseSVVLEEISVFPDGSPIS 390

WH1 domain; WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homolog. A subset of WH1 domains has been termed a "EVH1" domain and appear to bind a polyproline motif.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 102 QPIFSTRAHVFQIDPATKRNWIPAsKHALTVSYFYDATRNVYRIISVG--GTKAIINSTITPNMTFTKTSQKFGQWADSR 179
Cdd:pfam00568   9 QTICTAVAQVYLADPDNKRHWIKA-KHSGVVCFVKDSPQNSYFIRLVDiqDGKVIWNQEIYPNMEYNQARPFFHTFADSR 87

                          90       100
                  ....*....|....*....|....*.
gi 1561713857 180 AntVYGLGFASEQHLSQFAEKFQEVK 205
Cdd:pfam00568  88 C--VYGLNFASEEEATKFAKAVQEAL 111

WASP homology region 1; Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  101 EQPIFSTRAHVFQIDPATKRnWIPASKH-ALTVSYFYDATRNVYRIISV-GGTKAIINSTITPNMTFTKTSQKFGQWADs 178
Cdd:smart00461   3 SQCIILARAVVQLYDADTKK-WVPTGEGgAANLVIDKNQRSYFFRIVGIkGQDKVIWNQELYKNFKYNQATPTFHQWAD- 80

                           90       100
                   ....*....|....*....|....*
gi 1561713857  179 rANTVYGLGFASEQHLSQFAEKFQE 203
Cdd:smart00461  81 -DKCVYGLNFASEEEAKKFRKKVLK 104

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVS 61
Cdd:cd11257   404 LFLGTDDGRLHKAVSVGPMVHIIEELQIFSEGQPVQNLLLDTHKGLLYASSHSGVVQVPVA 464

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKgmLYVQSLSQVVQLPVS 61
Cdd:cd11260   398 MFIGTANGYVLKAVNYDGEMHIIEEVQLFEPEEPIDILRLSQNQ--LYAGSASGVVQMPVS 456

Enabled/VASP family EVH1 domain; Ena/VASP family includes proteins such as: Vasodilator-stimulated phosphoprotein (VASP), enabled gene product from Drosophila (Ena), mammalian enabled (Mena) and Ena/VASP-Like protein (EVL) localize to focal adhesions and to sites of actin filament dynamics. These proteins share a common modular organization with a highly conserved N- and C-terminal domains, termed Ena/VASP homology domains 1 and 2 (EVH1 and EVH2), that are separated by a central proline-rich domain. The EVH1 domain binds to other proteins at proline rich sequences. The majority of Ena-VASP type EVH1 domains recognize FPPPP motifs such as in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes, however the LIM3 domain of Tes lacks the FPPPP motif but still binds the EVH1 domain of Mena. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. EVH2 mediates oligomerization within the family. The proline-rich region binds SH3 and WW domains as well as profilin, a protein that regulates actin filament dynamics. The EVH1 domains are part of the PH domain superamily. There are 5 EVH1 subfamilies: Enables/VASP, Homer/Vesl, WASP, Dcp1, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 103 PIFSTRAHVFQIDPATKRnWIPA-SKHALTVSYFYDATR-NVYRIIsvgGTKA-----IINSTITPNMTFTKTSQKFGQW 175
Cdd:cd01207     1 SVASARASVMVYDDENKR-WVPSgGSQGLSRVQIYHNTRnNTFRVV---GRKLqdhevVINCAILKGLKYNQATPTFHQW 76

                          90       100
                  ....*....|....*....|...
gi 1561713857 176 ADSRanTVYGLGFASEQHLSQFA 198
Cdd:cd01207    77 RDAR--QVYGLNFASKEEATEFA 97

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKG--MLYVQSLSQVVQLPVS 61
Cdd:cd11259   409 MFISTDRGALHKAISLENEVHIIEETQLFPDFEPVQTLLLSSKKGrrFLYAGSNSGVVQSPLA 471

The Sema domain, a protein interacting module, of Plexin A2; Plexin A2 serves as a receptor for class 6 semaphorins. Interactions between Plexin A2, A4 and semaphorins 6A and 6B control the lamina-restricted projection of hippocampal mossy fibers. Sema6B also repels the growth of mossy fibers in a Plexin A4 dependent manner. Plexin A2 does not suppress Sema6B function. In addition, studies have shown that Plexin A2 may be related to anxiety and other psychiatric disorders. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857   1 MFLGTDDGYLHKaFNCDG---GMFVVEELQLFLSPEPV-RSLQLSAEKGMLYVQSLSQVVQLPVSECHQYKYCLDCILAR 76
Cdd:cd11272   409 VFVGTKSGKLKK-IRADGpphGGVQYEMVSVFKDGSPIlRDMAFSIDHKYLYVMSERQVSRVPVESCEQYTTCGECLSSG 487

                  ....*.
gi 1561713857  77 DPYCAW 82
Cdd:cd11272   488 DPHCGW 493

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLsaEKGMLYVQSLSQVVQLPVS 61
Cdd:cd11261   402 LYLGTEDGHLHRAVRIGAQLSVLEDLALFPEPQPVENLQL--HHNWLLVGSDTEVTQINTS 460

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 258 EITTEKERLKKMLSEGSVSEVQWEAEFFSLQDNNNKLVAALHEANANVDQWKKQLAAYQEETEMLRQRVAELESQGAHDs 337
Cdd:COG1196   250 ELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAEL- 328

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 338 ssENNKEELSQTLEELELLIKAKDEEIQmlksqkcgrwEAEGEREETLQKLQELEARNAELERRLHLAEQTLAETLAERE 417
Cdd:COG1196   329 --EEELEELEEELEELEEELEEAEEELE----------EAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAA 396

                         170
                  ....*....|.
gi 1561713857 418 KIQNEVTKVAE 428
Cdd:COG1196   397 ELAAQLEELEE 407

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMF------VVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVSEC 63
Cdd:cd11255   406 MFIGTDSGSVLKVIVLQKGNSaageevTLEELQVFKVPTPITEMEISVKRQMLYVGSRTGVAQVPLHRC 474

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1561713857   1 MFLGTDDGYLHKAF----NCDGGMFVVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPV 60
Cdd:cd11235   373 LFVGTDRGIILKVVslpeQGLQASNILEEMPVGPPPEPIQTMQLSRKRRSLYVGSETGVLQVPL 436

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857   1 MFLGTDDGYLHKAFNCDGG-MFVVEELQLFLSPEPVRSLQLSAEKGmlyvqslsqvvqlpvsechqykycldCILARDPY 79
Cdd:cd11256   386 MFLGTDKGFLHKAVLMGGSeSHIIEEIELLTPPEPVENLLLAANEG--------------------------VVYIGYSA 439

                  ...
gi 1561713857  80 CAW 82
Cdd:cd11256   440 GVW 442

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMFVVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPV 60
Cdd:cd11243   354 LYLATDKGKIHKVVESKGQTHNIMEIQPFKEQEPIQSMILDAERSHLYVGTKAEVTRLPL 413

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMF------VVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVSEC 63
Cdd:cd11250   403 MFIGTDVGSVLKVISVPKGSWpsneelLLEELHVFKDSSPITSMQISSKRQQLYVGSRSGVSQLPLHRC 471

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  260 TTEKERLKKMLSEGSVSEVQWEAEFFSLQDNNNKLVAALHEANANVDQWKKQLAAYQEETEMLRQRVAELESQGAH---- 335
Cdd:TIGR02168  231 VLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQIlrer 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  336 DSSSENNKEELS-------QTLEELELLIKAKDEEIQMLKSQKCgrwEAEGEREETLQKLQELEARNAELERRLHLAEQT 408
Cdd:TIGR02168  311 LANLERQLEELEaqleeleSKLDELAEELAELEEKLEELKEELE---SLEAELEELEAELEELESRLEELEEQLETLRSK 387

                          170
                   ....*....|....*
gi 1561713857  409 LAETLAEREKIQNEV 423
Cdd:TIGR02168  388 VAQLELQIASLNNEI 402

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  246 EDKLFRSQSADVEITTEKERLKKMLSEGSVSEVQWEAEFFSLQDNNNKLVAALHEANANVDQWKKQLAAYQEETEMLRQR 325
Cdd:TIGR02168  767 EERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQ 846

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  326 VAELESQGAHDSSSENNKEELSQTLE-ELELLIKAKDEEIQMLKSQKCGRWEAEGEREETLQKLQELEARNAELERRLHL 404
Cdd:TIGR02168  847 IEELSEDIESLAAEIEELEELIEELEsELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQ 926

                          170       180
                   ....*....|....*....|....*.
gi 1561713857  405 AEQTLAETLAEREKIQNEVTKVAEIM 430
Cdd:TIGR02168  927 LELRLEGLEVRIDNLQERLSEEYSLT 952

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857  298 LHEANANVDQWKKQLAAYQEETEMLRQRVAELESQgahDSSSENNKEELSQTLEELELLIKAKDEEIQmlksqkcgrwEA 377
Cdd:TIGR02169  296 IGELEAEIASLERSIAEKERELEDAEERLAKLEAE---IDKLLAEIEELEREIEEERKRRDKLTEEYA----------EL 362

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1561713857  378 EGEREETLQKLQELEARNAELERRLHLAEQTLAETLAEREKIQNEVTKVAEIMDVKIFELSEIRQGLAKLVE 449
Cdd:TIGR02169  363 KEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEA 434

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 317 EETEMLRQRVAELESQGAHDSSSENNKEELSQTLEELELLIKAKDEEIQMLKsQKCGRWEAEGEREETLQKLQELEARNA 396
Cdd:COG4717    71 KELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLE-KLLQLLPLYQELEALEAELAELPERLE 149

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1561713857 397 ELERRLhlaeQTLAETLAEREKIQNEVTKVAEIMD 431
Cdd:COG4717   150 ELEERL----EELRELEEELEELEAELAELQEELE 180

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 258 EITTEKERLKKMLSEGSVSEVQWEAEFFSLQDnnnklVAALHEANANVDQWKKQLAAYQEETEMLRQRVAELESQgahds 337
Cdd:COG4717    92 ELQEELEELEEELEELEAELEELREELEKLEK-----LLQLLPLYQELEALEAELAELPERLEELEERLEELREL----- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1561713857 338 ssENNKEELSQTLEELEllikakdEEIQMLKSQKcgRWEAEGEREETLQKLQELEARNAELERRLHLAEQTLAETLAERE 417
Cdd:COG4717   162 --EEELEELEAELAELQ-------EELEELLEQL--SLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEELE 230

                         170
                  ....*....|.
gi 1561713857 418 KIQNEVTKVAE 428
Cdd:COG4717   231 QLENELEAAAL 241

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1561713857   1 MFLGTDDGYLHKAFNCDGGMF-----VVEELQLFLSPEPVRSLQLSAEKGMLYVQSLSQVVQLPVSEC 63
Cdd:cd11252   407 MFLGTDIGTVLKVVSITKEKWtmeevVLEELQIFKHPSPILNMELSLKQQQLYIGSRDGLVQLSLHRC 474