Jump to navigation
Jump to search
m (Text replacement - "gene Genbank" to "gene RefSeq") |
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "") |
||
Line 1: | Line 1: | ||
__TOC__ | |||
<protect> | <protect> | ||
<aureodatabase> | <aureodatabase>annotation</aureodatabase> | ||
=Summary= | =Summary= | ||
* <aureodatabase>organism</aureodatabase> | *<aureodatabase>organism</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>pan locus</aureodatabase> | *<aureodatabase>pan locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>pan gene symbol</aureodatabase> | *<aureodatabase>pan gene symbol</aureodatabase> | ||
* <aureodatabase>gene synonyms</aureodatabase> | *<aureodatabase>gene synonyms</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
</protect> | </protect> | ||
Line 24: | Line 25: | ||
==General== | ==General== | ||
* <aureodatabase>gene type</aureodatabase> | *<aureodatabase>gene type</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
* <aureodatabase>gene replicon</aureodatabase> | *<aureodatabase>gene replicon</aureodatabase> | ||
* <aureodatabase>strand</aureodatabase> | *<aureodatabase>strand</aureodatabase> | ||
* <aureodatabase>gene coordinates</aureodatabase> | *<aureodatabase>gene coordinates</aureodatabase> | ||
* <aureodatabase>gene length</aureodatabase> | *<aureodatabase>gene length</aureodatabase> | ||
* <aureodatabase>essential</aureodatabase> | *<aureodatabase>essential</aureodatabase> | ||
*<aureodatabase>gene comment</aureodatabase> | |||
</protect> | </protect> | ||
Line 38: | Line 40: | ||
==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>gene GI</aureodatabase> | *<aureodatabase>gene GI</aureodatabase> | ||
* <aureodatabase>gene RefSeq</aureodatabase> | *<aureodatabase>gene RefSeq</aureodatabase> | ||
*<aureodatabase>gene BioCyc</aureodatabase> | |||
*<aureodatabase>gene MicrobesOnline</aureodatabase> | |||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Phenotype== | ==Phenotype== | ||
</protect> | </protect> | ||
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit§ion=6 edit]</span>] | |||
<protect> | <protect> | ||
==DNA sequence== | ==DNA sequence== | ||
* <aureodatabase>gene sequence</aureodatabase> | *<aureodatabase>gene sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
<aureodatabase>RNA regulated operons</aureodatabase> | |||
</protect> | |||
<protect> | |||
=Protein= | =Protein= | ||
<aureodatabase>protein 3D view</aureodatabase> | <aureodatabase>protein 3D view</aureodatabase> | ||
==General== | ==General== | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>protein symbol</aureodatabase> | *<aureodatabase>protein symbol</aureodatabase> | ||
* <aureodatabase>protein description</aureodatabase> | *<aureodatabase>protein description</aureodatabase> | ||
* <aureodatabase>protein length</aureodatabase> | *<aureodatabase>protein length</aureodatabase> | ||
* <aureodatabase>theoretical pI</aureodatabase> | *<aureodatabase>theoretical pI</aureodatabase> | ||
* <aureodatabase>theoretical MW</aureodatabase> | *<aureodatabase>theoretical MW</aureodatabase> | ||
* <aureodatabase>GRAVY</aureodatabase> | *<aureodatabase>GRAVY</aureodatabase> | ||
</protect> | </protect> | ||
Line 71: | Line 78: | ||
==Function== | ==Function== | ||
* <aureodatabase>protein reaction</aureodatabase> | *<aureodatabase>protein reaction</aureodatabase> | ||
* <aureodatabase>protein TIGRFAM</aureodatabase> | *<aureodatabase>protein TIGRFAM</aureodatabase> | ||
* <aureodatabase>protein TheSeed</aureodatabase> | *<aureodatabase>protein TheSeed</aureodatabase> | ||
* <aureodatabase>protein PFAM</aureodatabase> | *<aureodatabase>protein PFAM</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Structure, modifications & | ==Structure, modifications & cofactors== | ||
* <aureodatabase>protein domains</aureodatabase> | *<aureodatabase>protein domains</aureodatabase> | ||
* <aureodatabase>protein modifications</aureodatabase> | *<aureodatabase>protein modifications</aureodatabase> | ||
* <aureodatabase>protein cofactors</aureodatabase> | *<aureodatabase>protein cofactors</aureodatabase> | ||
* <aureodatabase>protein effectors</aureodatabase> | *<aureodatabase>protein effectors</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein regulated operons</aureodatabase> | ||
</protect> | </protect> | ||
Line 90: | Line 97: | ||
==Localization== | ==Localization== | ||
* <aureodatabase>protein Psortb</aureodatabase> | *<aureodatabase>protein Psortb</aureodatabase> | ||
* <aureodatabase>protein LocateP</aureodatabase> | *<aureodatabase>protein LocateP</aureodatabase> | ||
* <aureodatabase>protein SignalP</aureodatabase> | *<aureodatabase>protein SignalP</aureodatabase> | ||
* <aureodatabase>protein TMHMM</aureodatabase> | *<aureodatabase>protein TMHMM</aureodatabase> | ||
</protect> | </protect> | ||
Line 99: | Line 106: | ||
==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>protein GI</aureodatabase> | *<aureodatabase>protein GI</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein RefSeq</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein UniProt</aureodatabase> | ||
</protect> | </protect> | ||
Line 108: | Line 114: | ||
==Protein sequence== | ==Protein sequence== | ||
* <aureodatabase>protein sequence</aureodatabase> | *<aureodatabase>protein sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Experimental data== | ||
* <aureodatabase>protein validated peptides</aureodatabase> | *<aureodatabase>protein validated peptides</aureodatabase> | ||
*<aureodatabase>protein validated localization</aureodatabase> | |||
*<aureodatabase>protein validated quantitative data</aureodatabase> | |||
*<aureodatabase>protein partners</aureodatabase> | |||
</protect> | </protect> | ||
Line 125: | Line 134: | ||
==Operon== | ==Operon== | ||
* <aureodatabase>operons</aureodatabase> | *<aureodatabase>operons</aureodatabase> | ||
</protect> | </protect> | ||
Line 131: | Line 140: | ||
==Regulation== | ==Regulation== | ||
*<aureodatabase>regulators</aureodatabase> | |||
* <aureodatabase>regulators</aureodatabase> | |||
</protect> | </protect> | ||
Line 138: | Line 146: | ||
==Transcription pattern== | ==Transcription pattern== | ||
* <aureodatabase>expression browser</aureodatabase> | *<aureodatabase>expression browser</aureodatabase> | ||
</protect> | </protect> | ||
Line 144: | Line 152: | ||
==Protein synthesis (provided by Aureolib)== | ==Protein synthesis (provided by Aureolib)== | ||
* <aureodatabase>protein synthesis Aureolib</aureodatabase> | *<aureodatabase>protein synthesis Aureolib</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Protein stability== | ||
* <aureodatabase>protein half-life</aureodatabase> | *<aureodatabase>protein half-life</aureodatabase> | ||
</protect> | </protect> | ||
Latest revision as of 13:43, 10 March 2016
NCBI: 06-JUL-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus Newman
- locus tag: NWMN_0837 [new locus tag: NWMN_RS04720 ]
- pan locus tag?: SAUPAN003076000
- symbol: rexB
- pan gene symbol?: addB
- synonym:
- product: exonuclease RexB
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: NWMN_0837 [new locus tag: NWMN_RS04720 ]
- symbol: rexB
- product: exonuclease RexB
- replicon: chromosome
- strand: +
- coordinates: 925155..928631
- length: 3477
- essential: unknown other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 5332502 NCBI
- RefSeq: YP_001331871 NCBI
- BioCyc:
- MicrobesOnline: 3706386 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
- 1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
1681
1741
1801
1861
1921
1981
2041
2101
2161
2221
2281
2341
2401
2461
2521
2581
2641
2701
2761
2821
2881
2941
3001
3061
3121
3181
3241
3301
3361
3421ATGACATTACATGCTTATTTAGGTAGAGCGGGAACAGGTAAGTCTACGAAAATGTTGACC
GAAATAAAACAAAAAATGAAAGCAGATCCGCTTGGAGATCCAATCATTTTAATTGCGCCA
ACTCAAAGTACATTTCAATTAGAACAAGCCTTTGTCAATGATCCGGAATTAAATGGTAGT
TTAAGAACAGAAGTGTTGCATTTTGAACGATTAAGTCATCGTATTTTCCAAGAAGTTGGT
AGTTATAGCGAACAAAAGTTATCTAAAGCTGCAACGGAAATGATGATTTATAACATTGTT
CAAGAACAACAAAAGTATTTAAAACTTTATCAATCACAAGCAAAATATTATGGGTTTAGT
GAAAAATTAACAGAACAAATTCAAGATTTTAAAAAATATGCAGTAACGCCTGAACATTTA
GAACACTTTATTGCTGATAAAAATATGCAAACTCGAACTAAAAATAAGTTAGAGGATATT
GCTTTAATATACCGTGAGTTCGAACAACGCATTCAAAACGAGTTTATTACGGGTGAGGAT
TCATTACAATATTTTATTGATTGTATGCCGAAATCAGAGTGGCTAAAACGTGCTGATATA
TATATTGATGGTTTTCACAACTTTTCAACGATTGAGTATTTAATAATCAAAGGATTAATT
AAATATGCGAAGAGTGTCACAATTATATTGACGACAGATGGTAACCACGATCAATTTAGT
TTATTTAGAAAACCATCGGAAGTGTTACGACATATTGAAGAAATAGCAAATGAACTCAAT
ATTTCTATTGAACGTCAATATTTCAACCAATTATATCGCTTCAATAATCAAGATTTAAAG
CATCTTGAACAAGAATTTGATGCACTTCAAATCAATCGAGTGGCATGTCAAGGTCATATC
AATATTTTAGAATCTGCGACTATGAGAGAGGAAATAAATGAAATTGCGCGACGTATCATC
GTTGATATTCGTGATAAGCAATTACGATATCAAGATATTGCTATTTTATATCGTGATGAA
TCTTATGCTTATTTATTTGATTCCATATTACCGCTTTATAATATTCCTTATAATATTGAT
ACAAAGCGTTCGATGACACATCATCCGGTCATGGAAATGATTCGTTCATTGATTGAAGTT
ATTCAATCTAATTGGCAAGTGAATCCAATGCTACGCTTATTGAAGACTGATGTGTTAACG
GCATCATATCTAAAAAGTGCATACTTAGTTGATTTACTTGAAAATTTTGTACTTGAACGT
GGTATATACGGTAAACGTTGGTTAGATGATGAGCTATTTAATGTCGAACATTTTAGCAAA
ATGGGGCGTAAAGGGCATAAACTGACCGAAGATGAACGTAACACATTTGAACAAGTCGTT
AAGTTAAAGAAAGATGTCATTGATAAAATTTTACATTTTGAAAAGCAAATGTCACAAGCG
GAAACTGTAAAAGATTTTGCAACTGCTTTTTATGAAAGTATGGAATATTTCGAACTGCCA
AATCAATTGATGACAGAGCGAGATGAACTTGATTTAAATGGTAATCATGAAAAGGCGGAG
GAAATTGATCAAATATGGAATGGCTTAATTCAAATCCTTGATGACTTAGTTCTAGTATTT
GGAGATGAACCAATGTCGATGGAACGTTTCTTAGAAGTATTTGATATTGGTTTAGAACAA
TTAGAATTTGTTATGATTCCGCAAACATTGGACCAAGTAAGTATTGGTACGATGGATTTG
GCTAAAGTCGATAATAAGCAACATGTTTACTTAGTAGGTATGAATGATGGAACGATGCCA
CAACCAGTAACTGCGTCAAGCTTGATTACAGATGAAGAAAAGAAATACTTTGAACAGCAG
GCTAATGTCGAGTTAAGTCCAACATCAGATATTTTACAGATGGATGAAGCATTTGTTTGT
TATGTTGCTATGACTAGAGCTAAGGGAGATGTTACATTTTCTTACAGTCTAATGGGATCA
AGTGGTGATGATAAGGAGATCAGCCCATTTTTAAATCAAATTCAATCATTGTTCAACCAA
TTGGAAATTACTAACATTCCTCAATACCATGAAGTTAACCCATTGTCACTAATGCAACAT
GCTAAGCAAACCAAAATTACATTATTTGAAGCATTGCGTGCTTGGTTATATGATGAAATT
GTGGCTGATAGTTGGTTAGATGCTTATCAAGTAATTAGAGATAGCGATCATTTAAATCAA
GGTTTAGATTATTTAATGTCAGCATTAACGTTTGACAATGAAACTGTAAAATTAGGTGAA
ACGTTGTCTAAAGATTTATATGGTAAGGAAATCAATGCCAGTGTATCCCGTTTTGAAGGT
TATCAACAATGCCCATTTAAACACTATGCGTCACATGGTCTGAAACTAAATGAGCGAACG
AAGTATGAACTTCAAAACTTTGATTTAGGTGATATTTTCCATTCTGTTTTAAAATATATA
TCTGAACGTATTAATGGCGATTTTAAACAATTAGACCTGAAAAAAATAAGACAATTAACG
AATGAAGCATTGGAAGAAATTTTACCTAAAGTTCAGTTTAATTTATTAAATTCTTCAGCT
TACTATCGTTATTTATCAAGACGCATTGGCGCTATTGTAGAAACAACACTAAGCGCATTA
AAATATCAAGGCACGTATTCAAAGTTTATGCCAAAACATTTTGAGACAAGTTTTAGAAGG
AAACCAAGAACAAATGACGAATTAATTGCACAAACATTAACGACAACTCAAGGTATTCCA
ATTAATATTAGAGGGCAAATTGACCGTATCGATACGTATACAAAGAATGATACAAGTTTT
GTTAATATCATTGACTATAAATCCTCTGAAGGTAGTGCGACACTTGATTTAACGAAAGTA
TATTATGGTATGCAAATGCAAATGATGACATACATGGATATCGTTTTACAAAATAAACAA
CGCCTTGGATTAACAGATATTGTGAAACCAGGTGGATTATTATACTTCCATGTACATGAA
CCTAGAATTAAATTTAAATCATGGTCTGATATTGATGAAGATAAACTAGAACAAGATTTA
ATTAAAAAGTTTAAGTTGAGTGGTTTAGTTAATGCAGACCAAACTGTTATTGATGCATTG
GATATTCGTTTAGAACCTAAATTCACTTCAGATATTGTACCAGTTGGTTTGAATAAAGAT
GGCTCTTTGAGTAAACGAGGCAGCCAAGTGGCAGATGAAGCAACGATTTATAAATTCATC
CAACATAACAAAGAGAATTTTATAGAAACAGCTTCAAATATTATGGATGGACATACTGAA
GTTGCACCATTAAAGTACAAACAAAAATTGCCATGTGCTTTTTGTAGTTATCAATCGGTA
TGTCATGTAGATGGCATGATTGATAGTAAGCGATATCGAACTGTAGATGAAACAATAAAT
CCAATTGAAGCAATTCAAAATATTAACATTAATGATGAATTTGGGGGTGAGCAATAG60
120
180
240
300
360
420
480
540
600
660
720
780
840
900
960
1020
1080
1140
1200
1260
1320
1380
1440
1500
1560
1620
1680
1740
1800
1860
1920
1980
2040
2100
2160
2220
2280
2340
2400
2460
2520
2580
2640
2700
2760
2820
2880
2940
3000
3060
3120
3180
3240
3300
3360
3420
3477
⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: NWMN_0837 [new locus tag: NWMN_RS04720 ]
- symbol: RexB
- description: exonuclease RexB
- length: 1158
- theoretical pI: 5.06875
- theoretical MW: 134490
- GRAVY: -0.423575
⊟Function[edit | edit source]
- reaction: EC 3.6.4.12? ExPASyDNA helicase ATP + H2O = ADP + phosphateEC 3.1.-.-? ExPASy
- TIGRFAM: DNA metabolism DNA replication, recombination, and repair helicase-exonuclease AddAB, AddB subunit (TIGR02773; EC 3.1.-.-,3.6.4.12; HMM-score: 1417.2)and 5 moreDNA metabolism DNA replication, recombination, and repair ATP-dependent nuclease subunit B (TIGR02774; HMM-score: 173.6)probable DNA repair protein (TIGR03623; HMM-score: 32.4)DNA metabolism DNA replication, recombination, and repair ATP-dependent DNA helicase Rep (TIGR01074; EC 3.6.4.12; HMM-score: 30.1)DNA metabolism DNA replication, recombination, and repair double-strand break repair protein AddB (TIGR02786; HMM-score: 30)DNA metabolism DNA replication, recombination, and repair ATP-dependent DNA helicase PcrA (TIGR01073; EC 3.6.4.12; HMM-score: 14.2)
- TheSEED: data available for COL, N315, NCTC8325, USA300_FPR3757
- PFAM: PDDEXK (CL0236) PDDEXK_1; PD-(D/E)XK nuclease superfamily (PF12705; HMM-score: 174.4)and 3 moreP-loop_NTPase (CL0023) UvrD_C; UvrD-like helicase C-terminal domain (PF13361; HMM-score: 58.6)AAA_30; AAA domain (PF13604; HMM-score: 14.5)no clan defined Imm21; Immunity protein 21 (PF15589; HMM-score: 13)
⊟Structure, modifications & cofactors[edit | edit source]
- domains:
- modifications:
- cofactors: Mg2+, [4Fe-4S] cluster
- effectors:
⊟Localization[edit | edit source]
- PSORTb: Cytoplasmic
- Cytoplasmic Score: 7.5
- Cytoplasmic Membrane Score: 1.15
- Cellwall Score: 0.62
- Extracellular Score: 0.73
- Internal Helices: 0
- LocateP: Intracellular
- Prediction by SwissProt Classification: Cytoplasmic
- Pathway Prediction: No pathway
- Intracellular possibility: 1
- Signal peptide possibility: -1
- N-terminally Anchored Score: -1
- Predicted Cleavage Site: No CleavageSite
- SignalP: no predicted signal peptide
- SP(Sec/SPI): 0.002995
- TAT(Tat/SPI): 0.000315
- LIPO(Sec/SPII): 0.00049
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MTLHAYLGRAGTGKSTKMLTEIKQKMKADPLGDPIILIAPTQSTFQLEQAFVNDPELNGSLRTEVLHFERLSHRIFQEVGSYSEQKLSKAATEMMIYNIVQEQQKYLKLYQSQAKYYGFSEKLTEQIQDFKKYAVTPEHLEHFIADKNMQTRTKNKLEDIALIYREFEQRIQNEFITGEDSLQYFIDCMPKSEWLKRADIYIDGFHNFSTIEYLIIKGLIKYAKSVTIILTTDGNHDQFSLFRKPSEVLRHIEEIANELNISIERQYFNQLYRFNNQDLKHLEQEFDALQINRVACQGHINILESATMREEINEIARRIIVDIRDKQLRYQDIAILYRDESYAYLFDSILPLYNIPYNIDTKRSMTHHPVMEMIRSLIEVIQSNWQVNPMLRLLKTDVLTASYLKSAYLVDLLENFVLERGIYGKRWLDDELFNVEHFSKMGRKGHKLTEDERNTFEQVVKLKKDVIDKILHFEKQMSQAETVKDFATAFYESMEYFELPNQLMTERDELDLNGNHEKAEEIDQIWNGLIQILDDLVLVFGDEPMSMERFLEVFDIGLEQLEFVMIPQTLDQVSIGTMDLAKVDNKQHVYLVGMNDGTMPQPVTASSLITDEEKKYFEQQANVELSPTSDILQMDEAFVCYVAMTRAKGDVTFSYSLMGSSGDDKEISPFLNQIQSLFNQLEITNIPQYHEVNPLSLMQHAKQTKITLFEALRAWLYDEIVADSWLDAYQVIRDSDHLNQGLDYLMSALTFDNETVKLGETLSKDLYGKEINASVSRFEGYQQCPFKHYASHGLKLNERTKYELQNFDLGDIFHSVLKYISERINGDFKQLDLKKIRQLTNEALEEILPKVQFNLLNSSAYYRYLSRRIGAIVETTLSALKYQGTYSKFMPKHFETSFRRKPRTNDELIAQTLTTTQGIPINIRGQIDRIDTYTKNDTSFVNIIDYKSSEGSATLDLTKVYYGMQMQMMTYMDIVLQNKQRLGLTDIVKPGGLLYFHVHEPRIKFKSWSDIDEDKLEQDLIKKFKLSGLVNADQTVIDALDIRLEPKFTSDIVPVGLNKDGSLSKRGSQVADEATIYKFIQHNKENFIETASNIMDGHTEVAPLKYKQKLPCAFCSYQSVCHVDGMIDSKRYRTVDETINPIEAIQNININDEFGGEQ
⊟Experimental data[edit | edit source]
⊟Expression & Regulation[edit | edit source]
⊟Operon[edit | edit source]
⊟Regulation[edit | edit source]
- regulator:
⊟Transcription pattern[edit | edit source]
- S.aureus Expression Data Browser: data available for NCTC8325
⊟Protein synthesis (provided by Aureolib)[edit | edit source]
- Aureolib: no data available
⊟Protein stability[edit | edit source]
- half-life: no data available
⊟Biological Material[edit | edit source]
⊟Mutants[edit | edit source]
⊟Expression vector[edit | edit source]
⊟lacZ fusion[edit | edit source]
⊟GFP fusion[edit | edit source]
⊟two-hybrid system[edit | edit source]
⊟FLAG-tag construct[edit | edit source]
⊟Antibody[edit | edit source]
⊟Other Information[edit | edit source]
You are kindly invited to share additional interesting facts.