DOGAN: CDS Information : DMR

Display	Clone

Desulfovibrio magneticus RS-1 (= NBRC 104933) chromosome

Overview
Genome
Clone

Center position		change
ID		change
Gene name		change

Metabolism

Carbohydrate Metabolism

Glycolysis / Gluconeogenesis (00010)

Pyruvate metabolism (00620)

Glyoxylate and dicarboxylate metabolism (00630)

Propanoate metabolism (00640)

Butanoate metabolism (00650)

Inositol metabolism (00031)

Inositol phosphate metabolism (00562)

Citrate cycle (TCA cycle) (00020)

Pentose phosphate pathway (00030)

Fructose and mannose metabolism (00051)

Galactose metabolism (00052)

Ascorbate and aldarate metabolism (00053)

Starch and sucrose metabolism (00500)

Aminosugars metabolism (00530)

Nucleotide sugars metabolism (00520)

Energy Metabolism

electron transport system (00190)

ATP synthesis (00193)

Sulfur metabolism (00920)

ferredoxin, thioredoxin, rubredoxin

Lipid Metabolism

Fatty acid biosynthesis (path 1) (00061)

Fatty acid biosynthesis (path 2) (00062)

Fatty acid metabolism (00071)

Synthesis and degradation of ketone bodies (00072)

Sterols biosynthesis (00100)

Glycerolipid metabolism (00561)

Phospholipid degradation (00580)

Nucleotide Metabolism

Purine metabolism (00230)

Pyrimidine metabolism (00240)

Amino Acid Metabolism

Glutamate metabolism & Nitrogen assimilation (00910)

Arginine and proline metabolism (00330)

Histidine metabolism (00340)

Tyrosine metabolism (00350)

Phenylalanine metabolism (00360)

Tryptophan metabolism (00380)

Phenylalanine, tyrosine and tryptophan biosynthesis (00400)

Urea cycle and metabolism of amino groups (00220)

Alanine and aspartate metabolism (00252)

Glycine, serine and threonine metabolism (00260)

Methionine metabolism (00271)

Cysteine metabolism (00272)

Valine, leucine and isoleucine degradation (00280)

Valine, leucine and isoleucine biosynthesis (00660)

Lysine biosynthesis (00300)

Lysine degradation (00310)

Metabolism of Cofactors and Vitamins

Thiamine metabolism (00730)

Riboflavin metabolism (00740)

Vitamin B6 metabolism (00750)

Nicotinate and nicotinamide metabolism (00760)

Pantothenate and CoA biosynthesis (00770)

Biotin metabolism (00780)

Folate biosynthesis (00790)

Porphyrin and chlorophyll metabolism (00860)

Ubiquinone biosynthesis (00130)

Biosynthesis of Secondary Metabolites and Biodegradation of Xenobiotics

Degradation of aromatic compounds

Degradation of others

Others

Genetic Information Processing

Transcription

RNA polymerase (03020)

HTH family transcriptional regulators

sigma factor

Translation

Ribosome (03010)

Translation factors

Aminoacyl-tRNA biosynthesis (00970)

Replication and Repair

DNA polymerase (03030)

Replication complex

Others

Environmental Information and Cellular Processing

Membrane Transport (01310)

ABC transporter

transporters

Protein export

Phosphotransferase system (PTS)

Signal Transduction

Two-component system

Cellular Processes

Peptidoglycan biosynthesis (00550)

Cell wall/membrane/envelope biogenesis

Cell division

Cell Motility

Others

Unclassified

putative function (general)

uncharacterized protein

Transposon-related functions

hypothetical protein

hypothetical protein (prediction only)

Genome	Display	Sync
chromosome

Organism	Desulfovibrio magneticus RS-1 (= NBRC 104933)
Replicon	chromosome
Start / Stop / Direction	1,405,736 / 1,404,471 / -
Location	complement(1404471..1405736)
Type	CDS
Length	1,266 bp (421 aa)

Product	Fe hydrogenase large subunit
Gene name
Functional category	Metabolism - Energy Metabolism
EC number	1.12.7.2
Note	Contains one 4Fe-4S ferredoxin, iron-sulfur binding domain (IPR001450). Contains two Hydrogenase large subunit, C-terminal domain (IPR004108).
KEGG pathway	KO:K00532
Sequence feature
References	Family/Domain:IPR001450 Family/Domain:IPR004108 Uniprot:P07598 Pubmed:3888621

BLASTP
Database:UniProtKB:14.0

show BLAST table

1	E=0	PHFL_DESVO	Periplasmic [Fe] hydrogenase large subunit Fe hydrogenlyase	Alignment
2	E=0	PHFL_DESVH	Periplasmic [Fe] hydrogenase large subunit Fe hydrogenlyase	Alignment
3	E=0	A1VD88_DESVV	Hydrogenases, Fe-only	Alignment
4	E=0	Q317L4_DESDG	Ferredoxin hydrogenase	Alignment
5	E=0	Q9AM36_DESDE	[Fe] hydrogenase large subunit	Alignment

HAMAP

No significant hit

InterPro
Database:interpro:18.0

IPR001450 4Fe-4S ferredoxin, iron-sulfur binding (Conserved_site)
	PS00198 4FE4S_FER_1
IPR001450 4Fe-4S ferredoxin, iron-sulfur binding (Domain)
	PF00037 Fer4
	PS00198 4FE4S_FER_1
IPR001545 Gonadotropin, beta chain (Conserved_site)
	PS00261 GLYCO_HORMONE_BETA_1
IPR001545 Gonadotropin, beta chain (Family)
	PS00261 GLYCO_HORMONE_BETA_1
IPR004108 Hydrogenase large subunit, C-terminal (Domain)
	PF02906 Fe_hyd_lg_C
IPR009016 Iron hydrogenase (Domain)
	SSF53920 Fe-only hydrogenase
IPR013352 Hydrogenase, Fe-only (Domain)
	TIGR02512 Fe_only_hydrog: hydrogenases, Fe-only
IPR017896 4Fe-4S ferredoxin, iron-sulpur binding domain (Domain)
	PS51379 4FE4S_FER_2

SignalP

No significant hit

TMHMM

No significant hit

SOSUI

No significant hit

size of protein

421 amino acids

molecular mass

46,229.45 Da

pI

7.51

aa composition

Ala	Val	Leu	Ile	Phe	Trp	Pro	Met	Gly	Ser
8.6 (36aa)	7.6 (32aa)	5.2 (22aa)	4.5 (19aa)	4 (17aa)	1.9 (8aa)	5.9 (25aa)	4.5 (19aa)	9.7 (41aa)	4.5 (19aa)
Thr	Cys	Asn	Gln	Tyr	Lys	His	Arg	Asp	Glu
6.4 (27aa)	3.8 (16aa)	1.9 (8aa)	2.9 (12aa)	3.8 (16aa)	8.6 (36aa)	1.7 (7aa)	3.1 (13aa)	5.2 (22aa)	6.2 (26aa)

>DMR_12960 Fe hydrogenase large subunit
ATGAGCCGCGTTGAAATGGAGAAAATCTTCTACGAAATGCAGTCTCCGGACCCCAAGGCC
GATCCGGACAAGCTCTTCTTCATCAAGGTCGACGAGTCCAAATGCATCGGCTGCGACAGT
TGCATGGGCTATTGCCCCACCGGCGCCATCTACGGCGAGACCGGCGAACCTCACAAGATC
CCCCATGTCGAAGCCTGCATCAACTGTGGCCAGTGCCTCACCCACTGCCCGGTCTCGGCC
ATCTACGAAGAACAGTCCTGGGTTCCGGTCATCGAACAAAAGCTCAAGGATAAAAACGTC
AAGGTCATCGCCATGCCGGCCCCGGCCGTGCGCTACGGCCTGGGCGACTGCTTCGGCATG
CCCGTGGGCGCGGTGACCACGGACAAGATGCTCGGAGCCTTGCAAAAGCTCGGCTTTGAC
CACACCTGGGACAACGAGTGGACCGCCGACGTCACCATCTGGGAAGAAGGCTCGGAGTTC
GTCGGCCGGCTCACCAAAAAGATCGACAAGCCCCTGCCCCAGTTCACCTCCTGCTGTCCC
GGCTGGCACAAGTACGTCGAGACGTTCTATCCCGAGCTCTTCCCCAACATGTCCACCTGC
AAGTCCCCCATCGGGATGCTCGGCTCCCTGGCCAAGACCTACGGCGCGGACACCATGAAA
TACAAGCGCGCCGACGTCTTTACCGTCTCCATCATGCCCTGCACGGCCAAGAAATACGAA
GGCATGCGCCCGGCCAACTGGTCCAGCGGCTATCAGGACATCGACGCCACCATCGACACC
CGCGAACTGGCCTACATGTTCAAGAAAGCCGGCATCGACCTCAACACCGTGGCCCCGGGC
CAGCGCGACGCGCTCATGGGCGAGTCCACCGGCGGCGCCACCATCTTCGGCGTCACCGGC
GGCGTCATGGAAGCGGCCCTGCGCTACGCCTATCAGGCCGTCACCGGCAAGGCCCCGGAA
AGCTGGGACTTCAAGGCCGTGCGGGGGCTTAAGGGCCTCAAGGAAGCCACGGTCAATGTG
GGCGGCACGGACGTGAAGGTGGCCGTGGTCCACGGGGCCAAACGGTTCGCCGAGGTCTGC
GAAGTGGTCAAGGCCGGCAAGTCGCCCTGGCATTTCATCGAATTCATGGCCTGCCCCGGC
GGTTGCGTCATGGGCGGCGGCCAGCCCATCATGCCCGGCGTGCTGCAGTCCATGGATCGC
CGCACCACCAAATTCTACGCCTCGCTCAAAAAGCGCCTGGCCCTGTACAACGAACAAAAA
GCCTAA


>DMR_12960 Fe hydrogenase large subunit
MSRVEMEKIFYEMQSPDPKADPDKLFFIKVDESKCIGCDSCMGYCPTGAIYGETGEPHKI
PHVEACINCGQCLTHCPVSAIYEEQSWVPVIEQKLKDKNVKVIAMPAPAVRYGLGDCFGM
PVGAVTTDKMLGALQKLGFDHTWDNEWTADVTIWEEGSEFVGRLTKKIDKPLPQFTSCCP
GWHKYVETFYPELFPNMSTCKSPIGMLGSLAKTYGADTMKYKRADVFTVSIMPCTAKKYE
GMRPANWSSGYQDIDATIDTRELAYMFKKAGIDLNTVAPGQRDALMGESTGGATIFGVTG
GVMEAALRYAYQAVTGKAPESWDFKAVRGLKGLKEATVNVGGTDVKVAVVHGAKRFAEVC
EVVKAGKSPWHFIEFMACPGGCVMGGGQPIMPGVLQSMDRRTTKFYASLKKRLALYNEQK
A

NBRC No.	clone name	start	stop	length(bp)
G11-001-054	DM1GRC2E00013F07	1,394,395	1,431,063	36,669

We have been distributing copies of the microbial genomic DNA clones constructed during the course of each of the genomic DNA sequencing projects.
You can find more detailed information at http://www.nbrc.nite.go.jp/e/mdna-e.html.

CDS Information : DMR_12960

Genomic map

Desulfovibrio magneticus RS-1 (= NBRC 104933) chromosome

Location

Annotation

Computational search results

Calculated information (Amino acid sequence)

Sequence

Covered clones

Distribution of Our Microbial Genomic DNA clones