SNARE motif of syntaxin 12; Syntaxin 12 (STX12, also known as STX13 and STX14) forms a complex with SNAP25 (Qb/Qc) or SNAP29 (Qb/Qc) and VAMP2 or VAMP3 (R-SNARE) and plays a role in plasma membrane to early endosome transport. Syntaxin 12 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKKS 247
Cdd:cd15876   1 IKERETAIQQLEADILDVNQIFKDLAMMIHDQGDMIDSIEANVESAEVHVERASEQLQRAAYYQKKS 67

SNARE motif of syntaxin 12; Syntaxin 12 (STX12, also known as STX13 and STX14) forms a complex with SNAP25 (Qb/Qc) or SNAP29 (Qb/Qc) and VAMP2 or VAMP3 (R-SNARE) and plays a role in plasma membrane to early endosome transport. Syntaxin 12 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKKS 247
Cdd:cd15876   1 IKERETAIQQLEADILDVNQIFKDLAMMIHDQGDMIDSIEANVESAEVHVERASEQLQRAAYYQKKS 67

Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102  21 DFNSIIQTCSGNIQRISQATAQIKNLMSQLGTKQD-SSKLQENLQQLQHSTNQLAKETNELLKELGSLPLPLSA----SE 95
Cdd:cd00179   3 EFFEEVEEIRGNIDKISEDVEELQKLHSQLLTAPDaDPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEAlngsSV 82

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19527102  96 QRQQKLQKERLMNDFSSALNNFQVVQRKVSEKEKESIARARAGSRLSAEDRQREEQLVSFdSHEEWNQM 164
Cdd:cd00179  83 DRIRKTQHSGLSKKFVEVMTEFNKAQRKYRERYKERIQRQLEITGGEATDEELEDMLESG-NSEIFTSQ 150

t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102  96 QRQQKLQKERLMNDFSSALNNFQVVQRKVSEKEKESIARARAGSRLSA-----EDRQREEQLVSFDSHEEWNQMQSQEEE 170
Cdd:COG5325 103 NLQSSFLQSKLLRDLNTECMEGQRIQQKSAQFRKYQVLQAKFLRNKNNdqhplEEEEDEESLSSLGSQQTLQQQGLSNEE 182

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 171 AAITEQdleLIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKKSRKK 250
Cdd:COG5325 183 LEYQQI---LITERDEEIKNLARGIYELNEIFRDLGSLVGEQGELVDRIDFNIENTSDNLKNANKELEKAPAHQRRTKKC 259

SNARE domain; Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19527102   214 DLIDSIEANVESSEVHVERATDQLQRAAYYQKKSRKKMC 252
Cdd:pfam05739   1 EMLDRIDTNVENAQSNVERAQKELKKAVKYQKSNRKLKC 39

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 19527102     47 MSQLGTKQDSSKLQENLQQLQHSTNQLAKETNELLKELGSLplplsASEQRQQKLQKERLMNDFSSALNNFQVVqrkvse 126
Cdd:TIGR02168  670 SSILERRREIEELEEKIEELEEKIAELEKALAELRKELEEL-----EEELEQLRKELEELSRQISALRKDLARL------ 738

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102    127 kEKESIARARAGSRLSAEDRQREEQLVSFDSHEEWNQMQSQEEEAAITEQDlELIKERETAIRQLEADILDVNQIFKDLA 206
Cdd:TIGR02168  739 -EAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELE-AQIEQLKEELKALREALDELRAELTLLN 816

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 19527102    207 MMIHDQGDLIDSIEANVESSEVHVERATDQLQRAA 241
Cdd:TIGR02168  817 EEAANLRERLESLERRIAATERRLEDLEEQIEELS 851

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102  32 NIQRISQATAQIKNLMSQLGTKQdssKLQENLQQLQHSTNQLAKETNELLKELGSLPLPLSASEQRQQKLQKERLMNDFS 111
Cdd:COG4717  69 NLKELKELEEELKEAEEKEEEYA---ELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELP 145

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 112 SALNNFQVVQRKVSEKEKESIARARAGSRLSAEdRQREEQLVSFDSHEEWNQM----QSQEEEAAITEQDLELIKERETA 187
Cdd:COG4717 146 ERLEELEERLEELRELEEELEELEAELAELQEE-LEELLEQLSLATEEELQDLaeelEELQQRLAELEEELEEAQEELEE 224

                ...
gi 19527102 188 IRQ 190
Cdd:COG4717 225 LEE 227

SNARE motif of syntaxin 12; Syntaxin 12 (STX12, also known as STX13 and STX14) forms a complex with SNAP25 (Qb/Qc) or SNAP29 (Qb/Qc) and VAMP2 or VAMP3 (R-SNARE) and plays a role in plasma membrane to early endosome transport. Syntaxin 12 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKKS 247
Cdd:cd15876   1 IKERETAIQQLEADILDVNQIFKDLAMMIHDQGDMIDSIEANVESAEVHVERASEQLQRAAYYQKKS 67

SNARE motif of syntaxin 7, 12 and related sequences; SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. This subgroup of the Qa SNAREs includes syntaxin 7, syntaxin 12, TSNARE1 and related proteins.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRA 240
Cdd:cd15847   1 LLEREERIRQIESDILDVNQIFKDLATLVHEQGETIDSIEANIESAYVNVESGNSQLAKA 60

SNARE motif of syntaxin 7; Syntaxin 7 forms a complex with syntaxin 8 (Qc), Vti1b (Qb) and either VAMP7 or VAMP8 (R-SNARE) and is involved in the transport from early endosomes to the lysosome. Syntaxin 7 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRA 240
Cdd:cd15875   1 LEERERSIRQLESDIMDVNQIFKDLGMLVHEQGEVIDSIEANVETAAVHVEEANQQLSQA 60

SNARE motif, subgroup Qa; SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qa SNAREs are syntaxin 18, syntaxin 5, syntaxin 16, and syntaxin 1.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQR 239
Cdd:cd15840   1 IEEREEEIREIESSIGEVNEIFKDLATLVTEQGEQIDNIENNIEEAAANTEEANKELRK 59

SNARE motif of TSNARE1; TSNARE1 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. Its function is unknown, but polymorphisms in human TSNARE1 have been associated with schizophrenia susceptibility. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. TSNARE1 is part of a subgroup of the Qa SNAREs that also includes syntaxin 7, syntaxin 12 and related proteins.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19527102 178 LELIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAA 241
Cdd:cd15877   1 LEAIRQREEAIQQIESDMLDVNQIIKDLASMVSEQGDTIDSIEANIEAASSHVESANQQLAKAS 64

SNARE motif of syntaxin 16; Syntaxin 16 is located in trans-Golgi network (TGN) and regulated by the SM protein Vps45p. It forms a complex with syntaxin 6 (Qc), Vti1a (Qb) and VAMP4 (R-SNARE) and is involved in the regulation of recycling of early endosomes to the trans-Golgi network (TGN). Syntaxin 16 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQR 239
Cdd:cd15845   1 IQERDREIAKIVESINELAEIFKDLATLVIEQGTILDRIDYNIEQTATRVEKGVKELKK 59

SNARE domain; Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 19527102   214 DLIDSIEANVESSEVHVERATDQLQRAAYYQKKSRKKMC 252
Cdd:pfam05739   1 EMLDRIDTNVENAQSNVERAQKELKKAVKYQKSNRKLKC 39

SNARE motif of syntaxin 3; Syntaxin 3 (STX3) has been shown to form a complex with VAMP8 (R-SNARE) and SNAP-23 (Qb/c) in mast cells. Mutations have been implicated in human microvillus inclusion disease (MVID), a disorder of the differentiation of intestinal epithelium. Syntaxin 3 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19527102 178 LELIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQK 245
Cdd:cd15881   2 LSEIEGRHKDIVRLESSIKELHDMFVDIAMLVENQGEMLDNIELNVMKTVDHVEKARDETKKAVKYQS 69

SNARE motif of syntaxin 17; Synthaxin 17 (STX17) belongs to the Qa subgroup of SNAREs and interacts with SNAP29 (Qb/Qc) and the lysosomal R-SNARE VAMP8. The complex plays a role in autophagosome-lysosome fusion. Autophagosome transports cytoplasmic materials, including cytoplasmic proteins, glycogen, lipids, organelles, and invading bacteria to the lysosome for degradation. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19527102 175 EQDLELIKERETairqLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQR 239
Cdd:cd15846   2 PQRQACLESWET----LQQDLEDLHGLFTDFHQLVHDQGEQVDTIEDNVEEALENVQEGTKNLRK 62

t-SNARE complex subunit, syntaxin [Intracellular trafficking, secretion, and vesicular transport];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102  32 NIQRISQATAQIKNLMSQLGTKQD---SSKLQENLQQLQHSTNQLAKETNELLKELGSLPLPLSaseqrQQKLQKERLMN 108
Cdd:COG5074  33 NLSVYEKEINQIDNLHKDLLTEVFeeqSRKLRRSLDNFSSQTTDLQRNLKKDIKSAERDGIHLA-----NKQAQAENVRQ 107

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 109 DFSSALNNFQVVQRKVSEKEKESIARARAGSRLSAEDRQREEQLVSFDSHEEWNQMQSQEEEAAITEQDLELIKERETAI 188
Cdd:COG5074 108 KFLKLIQDYRIIDSNYREEEKEQARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNANRRGEAKTALAEVQARHQEI 187

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19527102 189 RQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQRAAYYQKKSRKK 250
Cdd:COG5074 188 KKIEKTMAELTQLFNDMEELVIEQQENVDVIDKNVEDAQENVEQGVGHTDKAVKSARAARKK 249

SNARE motif of syntaxin 4; Syntaxin-4 forms a complex with SNAP-23 (Qb/Qc) and R-SNAREs VAMP8, VAMP2 and VAMP7 which plays a role in exocytosis of secetory granule. Syntaxin 4 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19527102 178 LELIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQ 238
Cdd:cd15883   2 LNEIEARHSEIQKLERSIRELHDMFTYLAMEVEAQGEMIDRIEKNILSSADYVEKAQEHVK 62

SNARE motif of syntaxin 11; Syntaxin 11 (also known as STX11, FHL4, HLH4, HPLH4) is present on endosomal membranes, including late endosomes and lysosomes in macrophages, and has been shown to bind Vti1b and regulate the availability of Vti1b to form other SNARE-complexes. Mutations in human STX11 has been linked to familial hemophagocytic lymphohistiocytosis type-4 (FHL-4), an autosomal recessive disorder of immune dysregulation. Syntaxin 11 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19527102 181 IKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQR 239
Cdd:cd15878   5 IETRHKELLELESRIREVHELFLQMALLVEEQADTLNNIELNVEKTQDYVGKAKAQVKK 63

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 19527102     47 MSQLGTKQDSSKLQENLQQLQHSTNQLAKETNELLKELGSLplplsASEQRQQKLQKERLMNDFSSALNNFQVVqrkvse 126
Cdd:TIGR02168  670 SSILERRREIEELEEKIEELEEKIAELEKALAELRKELEEL-----EEELEQLRKELEELSRQISALRKDLARL------ 738

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102    127 kEKESIARARAGSRLSAEDRQREEQLVSFDSHEEWNQMQSQEEEAAITEQDlELIKERETAIRQLEADILDVNQIFKDLA 206
Cdd:TIGR02168  739 -EAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELE-AQIEQLKEELKALREALDELRAELTLLN 816

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 19527102    207 MMIHDQGDLIDSIEANVESSEVHVERATDQLQRAA 241
Cdd:TIGR02168  817 EEAANLRERLESLERRIAATERRLEDLEEQIEELS 851

Syntaxin; Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteriztic of and conserved in all syntaxins (pfam05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localization. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102    92 SASEQRQQKLQKERLMNDFSSALNNFQVVQRKVSEKEKESIAR---ARAGSRLSaedrqrEEQLVSFDSHEEWNQMQS-- 166
Cdd:pfam00804  83 GSAVDRIRRSQTAALRKKLKEVMAEYNELRERIREEYKEVIQRqyeTVTGKEVS------EEEIEEMIETGSESVFQKai 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 19527102   167 QEEEAAITEQDLELIKERETAIRQLEADILDVNQIFKDLAMMIHDQG 213
Cdd:pfam00804 157 LEQGRGQARSALSEIEERHKELKELESSLKELHQIFLDMAVLVEAQG 203

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102  32 NIQRISQATAQIKNLMSQLGTKQdssKLQENLQQLQHSTNQLAKETNELLKELGSLPLPLSASEQRQQKLQKERLMNDFS 111
Cdd:COG4717  69 NLKELKELEEELKEAEEKEEEYA---ELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELP 145

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19527102 112 SALNNFQVVQRKVSEKEKESIARARAGSRLSAEdRQREEQLVSFDSHEEWNQM----QSQEEEAAITEQDLELIKERETA 187
Cdd:COG4717 146 ERLEELEERLEELRELEEELEELEAELAELQEE-LEELLEQLSLATEEELQDLaeelEELQQRLAELEEELEEAQEELEE 224

                ...
gi 19527102 188 IRQ 190
Cdd:COG4717 225 LEE 227