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Conserved domains on  [gi|2427038561|ref|WP_270264314|]
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CAP domain-containing protein [Kocuria marina]

Protein Classification

SCP_bacterial and LGFP domain-containing protein( domain architecture ID 10143452)

SCP_bacterial and LGFP domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YkwD COG2340
Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell ...
 45-165 1.61e-20

Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell cycle control, cell division, chromosome partitioning, General function prediction only];


:

Pssm-ID: 441910  Cd Length: 144  Bit Score: 86.21  E-value: 1.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  45 AAPSDIVSVSSSTRAADAQKLLNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDHSNLF---LTDR-RAAGYN 120
Cdd:COG2340     4 ALLLAAAAAAPAALSALEQEVLELVNAYRAAAGLPPLTWDPRLTAAARAHAQDMAENGYFSHTGPDgssPFDRlKAAGYS 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2427038561 121 --AAGEIHALSwQNSVPDLMNWWKGSHAHNKVLTDPRMQVVGIGLTY 165
Cdd:COG2340    84 yrAAGENIAAG-YSTAEEAVDGWMNSPGHRANILNPDFTEIGVGVAY 129
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 222-342 1.87e-20

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 89.03  E-value: 1.87e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 222 APPAYTVKGGIKSRYQALGGAAKF-GYPTMNERGGLVNGGVYQNFraAGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAG 300
Cdd:COG5479   131 GTGAHAVHGAIRGKYAYHGWEDGPlGYPTSDEKATPDGGGRYQIF--EGGGIY---WSPATGAHAV--RGFIRGAWAALG 203

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2427038561 301 FERGW-GYPTTEEYRVGSEMRQRFSKGyTVHWSSVTGKTWVTR 342
Cdd:COG5479   204 WELGRlGYPTSDEYLVSGGRRQDFQGG-TITWAAATGAVRARA 245
 
Name Accession Description Interval E-value
YkwD COG2340
Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell ...
 45-165 1.61e-20

Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell cycle control, cell division, chromosome partitioning, General function prediction only];


Pssm-ID: 441910  Cd Length: 144  Bit Score: 86.21  E-value: 1.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  45 AAPSDIVSVSSSTRAADAQKLLNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDHSNLF---LTDR-RAAGYN 120
Cdd:COG2340     4 ALLLAAAAAAPAALSALEQEVLELVNAYRAAAGLPPLTWDPRLTAAARAHAQDMAENGYFSHTGPDgssPFDRlKAAGYS 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2427038561 121 --AAGEIHALSwQNSVPDLMNWWKGSHAHNKVLTDPRMQVVGIGLTY 165
Cdd:COG2340    84 yrAAGENIAAG-YSTAEEAVDGWMNSPGHRANILNPDFTEIGVGVAY 129
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 222-342 1.87e-20

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 89.03  E-value: 1.87e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 222 APPAYTVKGGIKSRYQALGGAAKF-GYPTMNERGGLVNGGVYQNFraAGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAG 300
Cdd:COG5479   131 GTGAHAVHGAIRGKYAYHGWEDGPlGYPTSDEKATPDGGGRYQIF--EGGGIY---WSPATGAHAV--RGFIRGAWAALG 203

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2427038561 301 FERGW-GYPTTEEYRVGSEMRQRFSKGyTVHWSSVTGKTWVTR 342
Cdd:COG5479   204 WELGRlGYPTSDEYLVSGGRRQDFQGG-TITWAAATGAVRARA 245
CAP_bacterial cd05379
Bacterial CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 ...
 62-162 2.01e-17

Bacterial CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain proteins; Little is known about bacterial and archaeal members of the CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain family. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. Studies of eukaryotic proteins show that CAP domains have several functions, including the binding of cholesterol, lipids and heparan sulfate. This group includes Borrelia burgdorferi outer surface protein BB0689, which does not bind to cholesterol, lipids, or heparan sulfate, and whose function is unknown.


Pssm-ID: 349398  Cd Length: 120  Bit Score: 77.03  E-value: 2.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  62 AQKLLNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDHSNLFLTDRRAA----GYNAAGEiHALSWQNSVPDL 137
Cdd:cd05379     1 EQEVLELINEYRAKAGLPPLSWDPRLEKAAQDHAEDMAANGYFSHTGPDGSSDRAAragyWYRGAGE-NIAYGQGSAEEA 79

                          90       100
                  ....*....|....*....|....*
gi 2427038561 138 MNWWKGSHAHNKVLTDPRMQVVGIG 162
Cdd:cd05379    80 VNQWINSPGHRANILDPDFTEIGVG 104
LGFP pfam08310
LGFP repeat; This 54 amino acid repeat is found in many hypothetical proteins. Several ...
 246-304 1.64e-13

LGFP repeat; This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesized that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. Deletion of Swiss:Q01377 protein results in a 10-fold increase in the cell volume of the organizm and infers the corresponding proteins involvement in the cell shape formation. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004].


Pssm-ID: 429909 [Multi-domain]  Cd Length: 53  Bit Score: 64.11  E-value: 1.64e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2427038561 246 GYPTMNERGGLVNGGVYQNFRaaGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAGFERG 304
Cdd:pfam08310   2 GYPTTDELATPDGGGRFQDFQ--GGSIY---WSPATGAHAV--RGAILDKWAALGWENG 53
CAP pfam00188
Cysteine-rich secretory protein family; This is a large family of cysteine-rich secretory ...
 66-162 3.48e-10

Cysteine-rich secretory protein family; This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organizms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilization. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences. The Ca++-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Swiss:Q91055 blocks the Ca++ transporting ryanodine receptors.


Pssm-ID: 395136  Cd Length: 117  Bit Score: 56.83  E-value: 3.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  66 LNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDH----SNLFLTDRRAAGYNAAGeihalSWQNSVPDLMNWW 141
Cdd:pfam00188   1 LDLHNEYRAAAGLPPLSWDNELAAAAQDHAKYCADNGSHNHrspyGGNIYARVVAAGYALGD-----AGPDSAEDAVDGW 75

                          90       100
                  ....*....|....*....|....*.
gi 2427038561 142 KGSHA-----HNKVLTDPRMQVVGIG 162
Cdd:pfam00188  76 YDSPGtyncgHRTNLLWPKSTKVGCA 101
 
Name Accession Description Interval E-value
YkwD COG2340
Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell ...
 45-165 1.61e-20

Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell cycle control, cell division, chromosome partitioning, General function prediction only];


Pssm-ID: 441910  Cd Length: 144  Bit Score: 86.21  E-value: 1.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  45 AAPSDIVSVSSSTRAADAQKLLNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDHSNLF---LTDR-RAAGYN 120
Cdd:COG2340     4 ALLLAAAAAAPAALSALEQEVLELVNAYRAAAGLPPLTWDPRLTAAARAHAQDMAENGYFSHTGPDgssPFDRlKAAGYS 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2427038561 121 --AAGEIHALSwQNSVPDLMNWWKGSHAHNKVLTDPRMQVVGIGLTY 165
Cdd:COG2340    84 yrAAGENIAAG-YSTAEEAVDGWMNSPGHRANILNPDFTEIGVGVAY 129
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 222-342 1.87e-20

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 89.03  E-value: 1.87e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 222 APPAYTVKGGIKSRYQALGGAAKF-GYPTMNERGGLVNGGVYQNFraAGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAG 300
Cdd:COG5479   131 GTGAHAVHGAIRGKYAYHGWEDGPlGYPTSDEKATPDGGGRYQIF--EGGGIY---WSPATGAHAV--RGFIRGAWAALG 203

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2427038561 301 FERGW-GYPTTEEYRVGSEMRQRFSKGyTVHWSSVTGKTWVTR 342
Cdd:COG5479   204 WELGRlGYPTSDEYLVSGGRRQDFQGG-TITWAAATGAVRARA 245
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 225-341 1.75e-18

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 83.25  E-value: 1.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 225 AYTVKGGIKSRYQALGGAAKF-GYPTMNERGGLVNGGVYQNFraAGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAGFER 303
Cdd:COG5479    27 AHAVRGAILAKYLALGGPRGLlGYPTTDELATPDGGGRYQRF--QNGSIY---WSPATGAHAV--VGAIRAKWGALGWES 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2427038561 304 GW-GYPTTEEYRVGSEMR-QRFSKGyTVHWSSVTGKTWVT 341
Cdd:COG5479   100 GPlGYPTTDEVPTPGGGRyQTFQGG-SVYWTAGTGAHAVH 138
CAP_bacterial cd05379
Bacterial CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 ...
 62-162 2.01e-17

Bacterial CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain proteins; Little is known about bacterial and archaeal members of the CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain family. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. Studies of eukaryotic proteins show that CAP domains have several functions, including the binding of cholesterol, lipids and heparan sulfate. This group includes Borrelia burgdorferi outer surface protein BB0689, which does not bind to cholesterol, lipids, or heparan sulfate, and whose function is unknown.


Pssm-ID: 349398  Cd Length: 120  Bit Score: 77.03  E-value: 2.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  62 AQKLLNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDHSNLFLTDRRAA----GYNAAGEiHALSWQNSVPDL 137
Cdd:cd05379     1 EQEVLELINEYRAKAGLPPLSWDPRLEKAAQDHAEDMAANGYFSHTGPDGSSDRAAragyWYRGAGE-NIAYGQGSAEEA 79

                          90       100
                  ....*....|....*....|....*
gi 2427038561 138 MNWWKGSHAHNKVLTDPRMQVVGIG 162
Cdd:cd05379    80 VNQWINSPGHRANILDPDFTEIGVG 104
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 174-341 1.24e-15

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 75.16  E-value: 1.24e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 174 GEGWRLVGTVDSY-GYPAGSgpsdvsRTVTAAAPRPQADTVAPVAAKRVAPPAYTVKGGIKSRYQALGGAAK-FGYPTMN 251
Cdd:COG5479    35 LAKYLALGGPRGLlGYPTTD------ELATPDGGGRYQRFQNGSIYWSPATGAHAVVGAIRAKWGALGWESGpLGYPTTD 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561 252 ERGGLvNGGVYQNFRaaGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAGFERG-WGYPTTEEYRV--GSEMRQRFSKGyT 328
Cdd:COG5479   109 EVPTP-GGGRYQTFQ--GGSVY---WTAGTGAHAV--HGAIRGKYAYHGWEDGpLGYPTSDEKATpdGGGRYQIFEGG-G 179

                         170
                  ....*....|...
gi 2427038561 329 VHWSSVTGKTWVT 341
Cdd:COG5479   180 IYWSPATGAHAVR 192
LGFP pfam08310
LGFP repeat; This 54 amino acid repeat is found in many hypothetical proteins. Several ...
 246-304 1.64e-13

LGFP repeat; This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesized that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. Deletion of Swiss:Q01377 protein results in a 10-fold increase in the cell volume of the organizm and infers the corresponding proteins involvement in the cell shape formation. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004].


Pssm-ID: 429909 [Multi-domain]  Cd Length: 53  Bit Score: 64.11  E-value: 1.64e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2427038561 246 GYPTMNERGGLVNGGVYQNFRaaGGAQYkfmWSPSSGAHVIkeTGAIGKRWKAAGFERG 304
Cdd:pfam08310   2 GYPTTDELATPDGGGRFQDFQ--GGSIY---WSPATGAHAV--RGAILDKWAALGWENG 53
CAP pfam00188
Cysteine-rich secretory protein family; This is a large family of cysteine-rich secretory ...
 66-162 3.48e-10

Cysteine-rich secretory protein family; This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organizms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilization. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences. The Ca++-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Swiss:Q91055 blocks the Ca++ transporting ryanodine receptors.


Pssm-ID: 395136  Cd Length: 117  Bit Score: 56.83  E-value: 3.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2427038561  66 LNLINQHRASKGLAPVKYSKSLSGIAQSQSDRLVKQEVIDH----SNLFLTDRRAAGYNAAGeihalSWQNSVPDLMNWW 141
Cdd:pfam00188   1 LDLHNEYRAAAGLPPLSWDNELAAAAQDHAKYCADNGSHNHrspyGGNIYARVVAAGYALGD-----AGPDSAEDAVDGW 75

                          90       100
                  ....*....|....*....|....*.
gi 2427038561 142 KGSHA-----HNKVLTDPRMQVVGIG 162
Cdd:pfam00188  76 YDSPGtyncgHRTNLLWPKSTKVGCA 101
Psp3 COG5479
LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane ...
 266-336 9.09e-05

LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 444230 [Multi-domain]  Cd Length: 246  Bit Score: 43.19  E-value: 9.09e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2427038561 266 RAAGGAQYKFMWSPSSGAHVIkeTGAIGKRWKAAGFERGW-GYPTTEEYR--VGSEMRQRFSKGyTVHWSSVTG 336
Cdd:COG5479    10 ADVPGRAQDFGWSPATGAHAV--RGAILAKYLALGGPRGLlGYPTTDELAtpDGGGRYQRFQNG-SIYWSPATG 80
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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