F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232  11 VVLRFMIFCRLLAKMANNDAVLKRLEQK-----------GAEADQIIEYLKQQVSLLKEKAILQATLREEKKLRVENAKL 79
Cdd:PRK08476  22 VILNSWLYKPLLKFMDNRNASIKNDLEKvktnssdvseiEHEIETILKNAREEANKIRQKAIAKAKEEAEKKIEAKKAEL 101

                         90
                 ....*....|.
gi 194384232  80 KKEIEELKQEL 90
Cdd:PRK08476 102 ESKYEAFAKQL 112

tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 174 IDVSRLDLRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMC 253
Cdd:cd02799    1 VDPSRLDIRVGKILKVRKHPDADSLYVEEIDLGEEEPRTIVSGLVKFVPLEQMQNRLVVVLCNLKPRKMRGVKSQGMVLC 80

                         90       100
                 ....*....|....*....|....*
gi 194384232 254 ASSP--EKIEILAPPNGSVPGDRIT 276
Cdd:cd02799   81 ASNAdhEKVELLEPPEGAKPGERVT 105

tRNA-binding EMAP/Myf domain [Translation, ribosomal structure and biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 175 DVSRLD-LRIGCIITARKHPDADSLYVEEVDVGEiAPRTVVSGLVNH-----VPlEQMQNRMVILLCNLKPAKMRGVLSQ 248
Cdd:COG0073   37 KVGGLDgLRVGKVLEAEPHPNADKLLVLQVDVGE-ETRQIVCGAPNVyagdkVP-EALVGAQVPGVVNLKPRKIRGVESE 114

                         90       100
                 ....*....|....*....|....*....
gi 194384232 249 AMVMCASSPEKIE----ILAPPNGSVPGD 273
Cdd:COG0073  115 GMLCSAEELGLGEdhdgILELPEDAPPGD 143

F0F1 ATP synthase subunit B'; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232  11 VVLRFMIFCRLLAKMANNDAVLKRLEQK-----------GAEADQIIEYLKQQVSLLKEKAILQATLREEKKLRVENAKL 79
Cdd:PRK08476  22 VILNSWLYKPLLKFMDNRNASIKNDLEKvktnssdvseiEHEIETILKNAREEANKIRQKAIAKAKEEAEKKIEAKKAEL 101

                         90
                 ....*....|.
gi 194384232  80 KKEIEELKQEL 90
Cdd:PRK08476 102 ESKYEAFAKQL 112

Basic leucine zipper (bZIP) domain of musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain; Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, and a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. The small Mafs (MafF, MafK, MafG) do not contain a transactivation domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. They play roles in stress response and detoxification pathways. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 194384232  49 LKQQVSLLKEKAILQATLreeKKLRVENAKLKKEIEELKQ 88
Cdd:cd14697   28 VQQKEQLENEKAELRSQI---EELKEENSELQQELDYYKQ 64

tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 174 IDVSRLDLRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMC 253
Cdd:cd02799    1 VDPSRLDIRVGKILKVRKHPDADSLYVEEIDLGEEEPRTIVSGLVKFVPLEQMQNRLVVVLCNLKPRKMRGVKSQGMVLC 80

                         90       100
                 ....*....|....*....|....*
gi 194384232 254 ASSP--EKIEILAPPNGSVPGDRIT 276
Cdd:cd02799   81 ASNAdhEKVELLEPPEGAKPGERVT 105

Putative tRNA binding domain; This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232  181 LRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMCAS--SPE 258
Cdd:pfam01588   1 LRVGKVVEAERHPNADKLLVCKVDVGEEEPRQIVSGAVNVYPPEELVGRLVVVVANLKPAKLRGVESEGMILSAEelDGG 80

                          90
                  ....*....|....*.
gi 194384232  259 KIEILAPPNGSVPGDR 274
Cdd:pfam01588  81 SVGLLEPPADVPPGTK 96

tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 175 DVSRLDLRIGCIITARKHPDADSLYVEEVDVGEiAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMCA 254
Cdd:cd02800    5 DFAKVDLRVGKVLEAERVEGSDKLLKLTVDLGE-EERQIVSGIAKFYPPEELVGKKVVVVANLKPRKLRGVESQGMILAA 83

                         90       100
                 ....*....|....*....|.
gi 194384232 255 SSPEKIEILAPPNGSVPGDRI 275
Cdd:cd02800   84 EDGGKLKLLTPDEEVEPGSRV 104

methionyl-tRNA synthetase; Reviewed

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 175 DVSRLDLRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMCA 254
Cdd:PRK12267 547 DFDKVELRVAEVLEAEKVEKSDKLLKLQVDLGEEEPRQIVSGIAKFYPPEELVGKKVVVVANLKPAKLMGEESQGMILAA 626

                         90       100
                 ....*....|....*....|.
gi 194384232 255 SSPEKIEILAPPNGSVPGDRI 275
Cdd:PRK12267 627 EDDGKLTLLTVDKEVPNGSKV 647

methionyl-tRNA synthetase C-terminal region/beta chain; The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should be called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model. [Protein synthesis, tRNA aminoacylation]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232  175 DVSRLDLRIGCIITARKHPDADSLYVEEVDVGEiAPRTVVSGLVNHVPLEQMQNRMVILLCNLKPAKMRGVLSQAMVMCA 254
Cdd:TIGR00399  36 DFEKVDLRVGKILKAERVEKSDKLLKLKLDLGD-EKRQIVSGIAGYYTPEELVGKKVIVVANLKPAKLFGVKSEGMILAA 114

                          90       100
                  ....*....|....*....|..
gi 194384232  255 -SSPEKIEILAPPNGSVPGDRI 275
Cdd:TIGR00399 115 eDDGKVLFLLSPDQEAIAGERI 136

tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs. This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232 181 LRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVpleqmQNRMVIL---------LCNLKPAKMRGVLSQAMv 251
Cdd:cd02796    1 VVVGKVLEVEPHPNADKLNVCKVDIGENKPLQIVCGAPNVR-----AGDKVVValpgavlpgGLKIKKRKLRGVESEGM- 74

                 ...
gi 194384232 252 MCA 254
Cdd:cd02796   75 LCS 77

F0F1 ATP synthase subunit B'; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194384232  11 VVLRFMIFCRLLAKMANNDAVLKRLEQK-----------GAEADQIIEYLKQQVSLLKEKAILQATLREEKKLRVENAKL 79
Cdd:PRK08476  22 VILNSWLYKPLLKFMDNRNASIKNDLEKvktnssdvseiEHEIETILKNAREEANKIRQKAIAKAKEEAEKKIEAKKAEL 101

                         90
                 ....*....|.
gi 194384232  80 KKEIEELKQEL 90
Cdd:PRK08476 102 ESKYEAFAKQL 112

Centrosomin N-terminal motif 1; This domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules. The pericentrin homolog Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB). Members of this family have been named centrosomins, and are an essential mitotic centrosome component required for assembly of all other known pericentriolar matrix proteins in order to achieve microtubule-organizing activity in fission yeast. Cnn_1N is a short conserved motif towards the N-terminus. Motif 1 is found to be necessary for proper recruitment of gamma-tubulin, D-TACC (the homolog of vertebrate transforming acidic coiled-coil proteins [TACC]), and Minispindles (Msps) to embryonic centrosomes but is not required for assembly of other centrosome components including Aurora A kinase and CP60 in Drosophila.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 194384232   46 IEYLKQQVSLLKEKAIlQATLREEKKLRVENAKLKKEIEELKQELIQAE 94
Cdd:pfam07989  21 IHFLEERLEKLAPEQI-EEALKENIELKVELETLQRELKKLKKLLREAE 68

Cell division protein ZapB; ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194384232   31 VLKRLEQKGAEADQIIEYLKQQVSLLKEKAilqATLREEKK-LRVENAKLKKEIEELKQELIQ 92
Cdd:pfam06005   5 LLEQLETKIQAAVDTIALLQMENEELKEEN---EELKEEANeLEEENQQLKQERNQWQERIRG 64

Basic leucine zipper (bZIP) domain of musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain; Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, and a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. The small Mafs (MafF, MafK, MafG) do not contain a transactivation domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. They play roles in stress response and detoxification pathways. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 194384232  49 LKQQVSLLKEKAILQATLreeKKLRVENAKLKKEIEELKQ 88
Cdd:cd14697   28 VQQKEQLENEKAELRSQI---EELKEENSELQQELDYYKQ 64