CAZyme Information: MGYG000003687_02222

Basic Information

• Species: Paenibacillus polymyxa
• Lineage: Bacteria; Firmicutes; Bacilli; Paenibacillales; Paenibacillaceae; Paenibacillus; Paenibacillus polymyxa
• CAZyme ID: MGYG000003687_02222
• CAZy Family: GT2
• CAZyme Description: Gramicidin S synthase 2

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
2849		319796.38	4.578

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003687	5656034	Isolate	China	Asia

• Gene Location: Start: 84219; End: 92768 Strand: +

Full Sequence      

MYDPLPKDESPSHSLNKDSELMTVTWTAQETEQLLKQAHRAYNTDMNDLLLTALGLAIHR
WAGIERVLVNLEGHGRESILPELDITRTVGWFTTQFPVVLDIGAGQDLSQRIKQVKEGLR
RIPQKGIGYGMLRYLSAACEQERFVTEPEISFNYLGQFDQDMQNQSIGVSPYASGAELSA
HAARSHTLDLNGLISEGQLQLTISYSHQEYRKETMEQLAEALRTSLQEIIAHCAGRKQQE
LTPSDVMLKPVTLAELDQLVERTRDIGEVENVYALTPMQKGMLFHSLMDAASGAYFEQTT
FDLRGRFQADIFQDSLNHLAQRHEIFRANFISGWQDEPVQVIFRRKDVGFSYEDLRHLDD
QERDAYVQEFIRQDKAAGFDLSRDALMRVAILRTGDEDYYFVWSSHHILMDGWCVALVTD
EVFEAYFAAVEHREPKLAPVTPYSQYIEWLEAQNVEAAASYWKDYLLGYDQQTSIPTGKV
GTKADGAQFEHVLCDLGKDLTGRLEMVAKQYHVTPNTLLQTAWGLLLQKYNGSDDAVFGG
VVSGRPADIPGIENMVGLFINTIPVRIRSGAEDTFADLIRTNQQQALASQDYETYPLYEI
QALTEQKQELINHIIVFENYPVEEQVEQLGEGAASDFVISNAGMIEQTNYDFNLVVMPQE
AMKIRFEYNTKLFDREAVERTQGHLIQLLEQVVAKPDIRVQELDVLSEQEREQILSVWGD
TAAEYPSEQTIHGLFETQTAHTPEQPALYFEGEQLSYRELNERANRLARTLRSQGVTKDR
LVGLMTERSVDLIVGMLGILKAGGAYVPIDPTYPEERIRYMLDDSGAKLLLTQGHLVDKV
AFDGHMLVLNGAQSVYHEDGSNLEPLSGPNDLAYVIYTSGTTGQPKGVMLEHHGLCNLKT
YFDQEFEISTSDHMLLFASYSFDAACWEIFQALFCGATLYVPTSETILDYERFEQYMADH
HITVAALPPTYAVYLEPQRMPNLRILVTAGSAASTELVYKWKDQVAYYNGYGPTENSVAT
SIWPVSKDERAGQLISIGRPVPNHRVYMVDVHGHLAPIGVAGELCVSGPGLARGYLDRPE
LTAEKFVPNPFAAGEAGYERMYRTGDLARWMPDGNIEYLGRIDHQVKIRGYRIELGEVEA
QILKVEDVQEVIVLAQADEQGQNQLVAYYVAEREVSAGELRSLLGEELPNYMVPSFLVQL
EQMPLTPNGKIDRKALPAPEGSLQTGANYVAPRTWVEVKLAQIWQDVLGLTQVGVKENFF
EIGGHSLRATTLASKIHKELNKPLPLRSIFEAPTIEQLAVVLEQLDQVTYASIPVTEERS
FYPLSSAQKRLYVLHQFDPQDVNYNMPSVLQVSGPLDVKRVEDVFRQLIARHATLRTRFD
LVDSEPVQSIEDTVPFEVEFTKVQAEGATTDTDTRVNKEVQELVSCFVRPFDLKAAPLLR
VGLVDLGVSGTEQEPQHVLMLDMHHIVSDGVSMGVLTNEFVRLYDGEQLAPLRIQYKDYA
VWQQSETHQEWMQRQEAYWLDTFRGELPVLDLPTDFARPSIRSTAGDTVVFGLEREVSER
LKELAAHTGSTLYMVLLAAYTALLHQYSGQEDIVVGTPIAGRPHADLEPILGMFVGTLAL
RNYPTAEHTFRSYVEEVKVQALQAYEHQDYPFEELVEKLNVKRDMSRHPLFDTMFTLQTT
EEGELQLADLSFRPYGLEQTPAKFDFTLEAREEEAGIQFGLQYATALYQRETVERMTRHF
IRLAEAVAANPDAKLGELELITTEETEQILKVFNDPNAHSVRGTLQGLSLSERFEEQAKN
SPERIAVVSGDIALTYAELNEQANRLARVLRAEGVEADQPVGVLLERSADLLVSILGVLK
AGGAYVPIDTMYPQERIDYMLQDSGAKVVITSRAANLSLSLPSTVQAIVLDDEDVQAQWG
AQDASNLIPVAGPHNLAYMIYTSGTTGQPKGVMIEQGSVGNLVDALYERVYSRYDHPLHI
AWLSAFVFDASVKQIFASLLLGHTLHVVSRDVSLSGEHLIAYYRTHRIDLSDGTPAHLHI
LNESVSVTEAPDVKHYLIGGEALSVQLVHVFLHKWSGYRPVITNVYGPTEATVDATAYTI
EDVESLNVLLEKGEHTVSIGTPIANQAVYILNTRQQLVPIGIAGELYIGGAGIARGYLNL
PELTAEKFVPNPFADATAADPADSTYANRMYRTGDLARWLPDGSIEYLGRIDHQVKIRGY
RIELGEVEAQLLTVDGIQKAVVTAWENEDGHKDLCAYIVASESLSLPELRNALQPKLPDY
MIPTYVVQLDRFPLTPNGKIDRKALPAPEARLEGGLEYVAPRTSLEAKLAQIWQDVLKLS
SVGVTDSFFDVGGHSLRATTLVAKIHQELGSRITLREVFQHFTIEQQAQLITAQGTDTYT
VIPAAAKQSYYPASSAQKRLYILSHLDGGEVSYNMPGVLVVEGPLQADRLEDAFRQLIAR
HETLRTSFEMVEGEVVQRVYDQVAFAVERLQAHESEAEAYIESFVRSFDLQQAPLLRVRL
IQTGPERHLLMYDMHHIISDGVSSNNIVQELGQLYEGQALAPLPIQYKDYAVWQQQEMQR
ESYQRREQFWLEHLAGELPVLELPIAYPRPAVRSFEGAMYEFTVDPNVSEQLRRIATQTG
STLYMVLLSAYTVLLSKYSGQDDLIIGTPVAGRLLPELEPLIGMFVNTLAIRHQPQGNQT
FHSYLLEARERTLQAFEHQDYPLEELVEKLDVARDASRNPLFDTMFVLQNTESQEAKLET
LSFSPYVQEHRISKFDLTLSMSDEDGQIKGSFEYCTKLFGVDAIERLTGDLIAILSQVGA
NPDLLLSDIQVNSSEQPEGFSPDSIDFIF

Enzyme Prediction     

No EC number prediction in MGYG000003687_02222.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd19543	DCL_NRPS	0.0	272	696	1	423	DCL-type Condensation domain of nonribosomal peptide synthetases (NRPSs), which catalyzes the condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. The DCL-type Condensation (C) domain catalyzes the condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. This domain is D-specific for the peptidyl donor and L-specific for the aminoacyl acceptor ((D)C(L)); this is in contrast with the standard LCL domains which catalyze peptide bond formation between two L-amino acids, and the restriction of ribosomes to use only L-amino acids. C domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains in addition to the LCL- and DCL-types such as starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity.
cd19531	LCL_NRPS-like	0.0	1322	1751	2	427	LCL-type Condensation (C) domain of non-ribosomal peptide synthetases(NRPSs) and similar domains including the C-domain of SgcC5, a free-standing NRPS with both ester- and amide- bond forming activity. LCL-type Condensation (C) domains catalyze peptide bond formation between two L-amino acids, ((L)C(L)). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to the LCL-type, there are various subtypes of C-domains such as the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. Streptomyces globisporus SgcC5 is a free-standing NRPS condensation enzyme (rather than a modular NRPS), which catalyzes the condensation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1phenyl-1,2-ethanediol, forming an ester bond, during the synthesis of the chromoprotein enediyne antitumor antibiotic C-1027. It has some acceptor substrate promiscuity as it has been shown to also catalyze the formation of an amide bond between SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and a mimic of the enediyne core acceptor substrate having an amine at its C-2 position. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. An HHxx[SAG]DGxSx(6)[ED] motif is characteristic of LCL-type C-domains.
cd12117	A_NRPS_Srf_like	0.0	734	1216	2	483	The adenylation domain of nonribosomal peptide synthetases (NRPS), including Bacillus subtilis termination module Surfactin (SrfA-C). The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the adenylation domain of the Bacillus subtilis termination module (Surfactin domain, SrfA-C) which recognizes a specific amino acid building block, which is then activated and transferred to the terminal thiol of the 4'-phosphopantetheine (Ppan) arm of the downstream peptidyl carrier protein (PCP) domain.
PRK12316	PRK12316	0.0	3	1308	3834	5145	peptide synthase; Provisional
cd19531	LCL_NRPS-like	0.0	2410	2822	1	427	LCL-type Condensation (C) domain of non-ribosomal peptide synthetases(NRPSs) and similar domains including the C-domain of SgcC5, a free-standing NRPS with both ester- and amide- bond forming activity. LCL-type Condensation (C) domains catalyze peptide bond formation between two L-amino acids, ((L)C(L)). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to the LCL-type, there are various subtypes of C-domains such as the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. Streptomyces globisporus SgcC5 is a free-standing NRPS condensation enzyme (rather than a modular NRPS), which catalyzes the condensation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1phenyl-1,2-ethanediol, forming an ester bond, during the synthesis of the chromoprotein enediyne antitumor antibiotic C-1027. It has some acceptor substrate promiscuity as it has been shown to also catalyze the formation of an amide bond between SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and a mimic of the enediyne core acceptor substrate having an amine at its C-2 position. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. An HHxx[SAG]DGxSx(6)[ED] motif is characteristic of LCL-type C-domains.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QND46664.1	0.0	231	2436	518	2702
BAY90071.1	1.61e-197	365	2838	228	2680
ACX49739.1	6.41e-197	275	2071	12	1847
BAZ00088.1	2.26e-190	365	2829	229	2680
BAZ75991.1	2.26e-190	365	2829	229	2680

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
6MFY_A	0.0	724	2309	200	1716	Crystalstructure of a 5-domain construct of LgrA in the substrate donation state [Brevibacillus parabrevis],6MG0_A Crystal structure of a 5-domain construct of LgrA in the thiolation state [Brevibacillus parabrevis],6MG0_B Crystal structure of a 5-domain construct of LgrA in the thiolation state [Brevibacillus parabrevis]
6MFZ_A	0.0	724	2411	200	1813	Crystalstructure of dimodular LgrA in a condensation state [Brevibacillus parabrevis],6MFZ_B Crystal structure of dimodular LgrA in a condensation state [Brevibacillus parabrevis]
2VSQ_A	5.69e-235	268	1356	8	1114	Structureof surfactin A synthetase C (SrfA-C), a nonribosomal peptide synthetase termination module [Bacillus subtilis]
5U89_A	2.01e-209	1764	2836	5	1066	Crystalstructure of a cross-module fragment from the dimodular NRPS DhbF [Geobacillus sp. Y4.1MC1]
6MFW_A	6.98e-206	724	1765	200	1205	Crystalstructure of a 4-domain construct of LgrA in the substrate donation state [Brevibacillus parabrevis]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P45745	0.0	273	2389	9	2105	Dimodular nonribosomal peptide synthase OS=Bacillus subtilis (strain 168) OX=224308 GN=dhbF PE=1 SV=4
Q70LM4	0.0	5	2391	2313	4672	Linear gramicidin synthase subunit D OS=Brevibacillus parabrevis OX=54914 GN=lgrD PE=1 SV=1
Q04747	0.0	269	2829	6	2515	Surfactin synthase subunit 2 OS=Bacillus subtilis (strain 168) OX=224308 GN=srfAB PE=1 SV=3
P94459	0.0	267	2836	5	2514	Plipastatin synthase subunit D OS=Bacillus subtilis (strain 168) OX=224308 GN=ppsD PE=1 SV=2
Q70LM5	0.0	4	2821	4915	7719	Linear gramicidin synthase subunit C OS=Brevibacillus parabrevis OX=54914 GN=lgrC PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000040	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000003687_02222.