Assessing expression of methylation genes
Goal: extract blast hits to DNMT3a, DNMT1, TET1 in Mcap and Pdam
Proteins of Interest
>sp|Q1LZ53|DNM3A_RAT DNA (cytosine-5)-methyltransferase 3A OS=Rattus norvegicus OX=10116 GN=Dnmt3a PE=1 SV=1
MPSSGPGDTSISSLEREDDRKEGEEQEENRGKEERQEPSATARKVGRPGRKRKHPPVESS
DTPKDPAVTTKSQPTAQDSGPSDLLPNGDLEKRSEPQPEEGSPAAGQKGGAPAEGEGTET
PPEASRAVENGCCVTKEGRGASAGEGKEQKQTNIESMKMEGSRGRLRGGLGWESSLRQRP
MPRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAVMNAVEESQASGESQKVEEASP
PAVQQPTDPASPTVATTPEPVGADAGDKNATKAADDEPEYEDGRGFGIGELVWGKLRGFS
WWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPM
YRKAIYEVLQVASSRAGKLFPACHDSDESDTGKAVEVQNKQMIEWALGGFQPSGPKGLEP
PEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTTEKPKVKEIIDERTRERLVYEVR
QKCRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGR
EVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSR
LQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASE
VCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLY
EGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKE
VSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGK
DQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAP
LKEYFACV
>sp|Q92072|DNMT1_CHICK DNA (cytosine-5)-methyltransferase 1 OS=Gallus gallus OX=9031 GN=DNMT1 PE=1 SV=1
MPARSAPPPPALPPALRRRLRDLERDEDSLSEKETLQEKLRLTRGFLRAEVQRRLSALDA
DVRCRELSEERYLAKVKALLRRELAAENGDAAKLFSRASNGCAGNGEEEWERGGRGEDGA
MEVEEAAASSSSSSSSSSSSSSSSSSSSSLLPAPRARKARRSRSNGESKKSPASSRVTRS
SGRQPTILSVFSKGSTKRKSEEVNGAVKPEVSAEKDEEEEEELEEKEQDEKRIKIETKEG
SEIKDEITQVKTSTPAKTTPPKCVDCRQYLDDPDLKFFQGDPDDALEEPEMLTDERLSIF
DANEDGFESYEDLPQHKVTSFSVYDKRGHLCPFDTGLIERNIELYFSGAVKPIYDDNPCL
DGGVRAKKLGPINAWWITGFDGGEKALIGFTTAFADYILMEPSEEYAPIFALMQEKIYMS
KIVVEFLQNNRDVSYEDLLNKIETTVPPVGLNFNRFTEDSLLRHAQFVVEQVESYDEAGD
SDEPPVLITPCMRDLIKLAGVTLGKRRAVRRQAIRHPTRIDKDKGPTKATTTKLVYLIFD
TFFSEQIEKDEREDDKENAMKRRRCGVCEVCQQPECGKCKACQNMVKFGGSGRSKQACLQ
RRCPNLAVREADEDEEVDDNIPEMPSPKKMLQGRKKKQNKSRISWVGEPIKSDGKKDFYQ
RVCIDSETLEVGDCVSVSPDDPTKPLYLARVTAMWEDSSGQMFHAHWFCPGSDTVLGATS
DPLELFLVDECEDMQLSYIHGKVNVIYKPPSENWAMEGGLDMEIKMVEDDGRTYFYQMWY
DQEYARFETPPRAQPMEDNKYKFCLSCARLDEVRHKEIPKVAEPLDEGDGKMFYAMATKN
GVQYRVGDSVYLLPEAFSFSMKPASPAKRPKKEAVDEDLYPEHYRKYSEYIKGSNLDAPD
PYRVGRIKEIFCHIRTNGKPNEADIKLRIWKFYRPENTHKSMKATYHADINLLYWSDEET
TVDFCAVQGRCTVVYGEDLTESIQDYSAGGLDRFYFLEAYNAKTKSFEDPPNHARSSGNK
GKGKGKGKGKGKGKSSTTCEQSEPEPTELKLPKLRTLDVFSGCGGLSEGFHQAGVSETLW
AIEMWEPAAQAFRLNNPGTTVFTEDCNVLLKLVMSGEKTNSLGQKLPQKGDVEMLCGGPP
CQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLR
CLVRMGYQCTFGVLQAGQYGVAQTRRRAIVLAAAPGEKLPMFPEPLHVFAPRACQLSVVV
DDKKFVSNITRTYSGPFRTITVRDTMSDLPEIRNGASALEISYNGEPQSWFQRQIRGSQY
QPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTSTRKLRYTHHEKKNG
RSSSGALRGVCSCAEGKPCDPADRQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTT
VTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAK
AIGLEIRACVGARMREESGAAVAPPAPEKMEMTAAAD
>sp|Q3URK3|TET1_MOUSE Methylcytosine dioxygenase TET1 OS=Mus musculus OX=10090 GN=Tet1 PE=1 SV=2
MSRSRPAKPSKSVKTKLQKKKDIQMKTKTSKQAVRHGASAKAVNPGKPKQLIKRRDGKKE
TEDKTPTPAPSFLTRAGAARMNRDRNQVLFQNPDSLTCNGFTMALRRTSLSWRLSQRPVV
TPKPKKVPPSKKQCTHNIQDEPGVKHSENDSVPSQHATVSPGTENGEQNRCLVEGESQEI
TQSCPVFEERIEDTQSCISASGNLEAEISWPLEGTHCEELLSHQTSDNECTSPQECAPLP
QRSTSEVTSQKNTSNQLADLSSQVESIKLSDPSPNPTGSDHNGFPDSSFRIVPELDLKTC
MPLDESVYPTALIRFILAGSQPDVFDTKPQEKTLITTPEQVGSHPNQVLDATSVLGQAFS
TLPLQWGFSGANLVQVEALGKGSDSPEDLGAITMLNQQETVAMDMDRNATPDLPIFLPKP
PNTVATYSSPLLGPEPHSSTSCGLEVQGATPILTLDSGHTPQLPPNPESSSVPLVIAANG
TRAEKQFGTSLFPAVPQGFTVAAENEVQHAPLDLTQGSQAAPSKLEGEISRVSITGSADV
KATAMSMPVTQASTSSPPCNSTPPMVERRKRKACGVCEPCQQKANCGECTYCKNRKNSHQ
ICKKRKCEVLKKKPEATSQAQVTKENKRPQREKKPKVLKTDFNNKPVNGPKSESMDCSRR
GHGEEEQRLDLITHPLENVRKNAGGMTGIEVEKWAPNKKSHLAEGQVKGSCDANLTGVEN
PQPSEDDKQQTNPSPTFAQTIRNGMKNVHCLPTDTHLPLNKLNHEEFSKALGNNSSKLLT
DPSNCKDAMSVTTSGGECDHLKGPRNTLLFQKPGLNCRSGAEPTIFNNHPNTHSAGSRPH
PPEKVPNKEPKDGSPVQPSLLSLMKDRRLTLEQVVAIEALTQLSEAPSESSSPSKPEKDE
EAHQKTASLLNSCKAILHSVRKDLQDPNVQGKGLHHDTVVFNGQNRTFKSPDSFATNQAL
IKSQGYPSSPTAEKKGAAGGRAPFDGFENSHPLPIESHNLENCSQVLSCDQNLSSHDPSC
QDAPYSQIEEDVAAQLTQLASTINHINAEVRNAESTPESLVAKNTKQKHSQEKRMVHQKP
PSSTQTKPSVPSAKPKKAQKKARATPHANKRKKKPPARSSQENDQKKQEQLAIEYSKMHD
IWMSSKFQRFGQSSPRSFPVLLRNIPVFNQILKPVTQSKTPSQHNELFPPINQIKFTRNP
ELAKEKVKVEPSDSLPTCQFKTESGGQTFAEPADNSQGQPMVSVNQEAHPLPQSPPSNQC
ANIMAGAAQTQFHLGAQENLVHQIPPPTLPGTSPDTLLPDPASILRKGKVLHFDGITVVT
EKREAQTSSNGPLGPTTDSAQSEFKESIMDLLSKPAKNLIAGLKEQEAAPCDCDGGTQKE
KGPYYTHLGAGPSVAAVRELMETRFGQKGKAIRIEKIVFTGKEGKSSQGCPVAKWVIRRS
GPEEKLICLVRERVDHHCSTAVIVVLILLWEGIPRLMADRLYKELTENLRSYSGHPTDRR
CTLNKKRTCTCQGIDPKTCGASFSFGCSWSMYFNGCKFGRSENPRKFRLAPNYPLHEKQL
EKNLQELATVLAPLYKQMAPVAYQNQVEYEEVAGDCRLGNEEGRPFSGVTCCMDFCAHSH
KDIHNMHNGSTVVCTLIRADGRDTNCPEDEQLHVLPLYRLADTDEFGSVEGMKAKIKSGA
IQVNGPTRKRRLRFTEPVPRCGKRAKMKQNHNKSGSHNTKSFSSASSTSHLVKDESTDFC
PLQASSAETSTCTYSKTASGGFAETSSILHCTMPSGAHSGANAAAGECTGTVQPAEVAAH
PHQSLPTADSPVHAEPLTSPSEQLTSNQSNQQLPLLSNSQKLASCQVEDERHPEADEPQH
PEDDNLPQLDEFWSDSEEIYADPSFGGVAIAPIHGSVLIECARKELHATTSLRSPKRGVP
FRVSLVFYQHKSLNKPNHGFDINKIKCKCKKVTKKKPADRECPDVSPEANLSHQIPSRVA
STLTRDNVVTVSPYSLTHVAGPYNRWV
Make Mcap blastdb
/Applications/ncbi-blast-2.6.0+/bin/makeblastdb -in /Users/hputnam/MyProjects/Holobiont_Integration/RAnalysis/Data/Transcriptomics/Mcapitata_holotranscriptome_data_v1/Montipora_capitata_v1_gene_models_coding.pep.faa -dbtype prot
Blast Uniprot proteins against all Mcap coding gene models
/Applications/ncbi-blast-2.6.0+/bin/blastp -query /Users/hputnam/MyProjects/Mcap_Genome/Mcap_Genome_Files/DNMTs_TET.fa \
-db Montipora_capitata_v1_gene_models_coding.pep.faa \
-outfmt 6 \
-max_target_seqs 10 \
-evalue 1e-05 \
-out Mcap_DNMT_TET_hits_10
Mcap Results
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
DNMT3A sp|Q1LZ53|DNM3A_RAT Montipora_capitata_PredGene_g25804.t1 47.251 673 313 9 267 907 50 712 0.0 622
DNMT3A sp|Q1LZ53|DNM3A_RAT Montipora_capitata_PredGene_g25804.t1.1.5eba3f22 49.393 577 255 7 360 907 4 572 0.0 563
DNMT3A sp|Q1LZ53|DNM3A_RAT Montipora_capitata_PredGene_g25804.t1.1.5eba3f22.1.5ebd33c4 56.808 426 166 5 489 907 21 435 3.11e-163 485
DNMT3A sp|Q1LZ53|DNM3A_RAT Montipora_capitata_PASA_asmbl_302557.p1 31.492 181 97 4 267 422 50 228 1.94e-22 99.4
DNMT3A sp|Q1LZ53|DNM3A_RAT Montipora_capitata_PredGene_adi2mcaRNA26694_R0.t1 52.542 59 28 0 286 344 1316 1374 1.01e-12 74.3
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PredGene_g53952.t1 55.818 1564 566 22 44 1512 2 1535 0.0 1686
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_419305.p1 43.407 1039 467 21 12 958 8 1017 0.0 812
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_419313.p1 42.857 819 357 17 12 748 8 797 0.0 617
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_419303.p2 41.379 87 45 2 746 826 1 87 1.15e-14 72.8
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_419302.p2 41.379 87 45 2 746 826 1 87 1.15e-14 72.8
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PredGene_g48416.t1.1.5eba4405 30.952 168 96 7 443 606 366 517 8.04e-11 68.6
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PredGene_g48416.t1 30.952 168 96 7 443 606 366 517 8.04e-11 68.6
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_346455.p1 30.952 168 96 7 443 606 323 474 8.57e-11 68.6
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_346456.p1 30.952 168 96 7 443 606 323 474 1.97e-10 67.8
DNMT1 sp|Q92072|DNMT1_CHICK Montipora_capitata_PASA_asmbl_346460.p1 30.952 168 96 7 443 606 287 438 2.00e-10 67.8
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1.1.5eba4300 54.698 298 128 5 1367 1664 208 498 2.42e-96 345
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1.1.5eba4300 58.333 72 25 1 1885 1956 783 849 3.02e-13 77.4
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1.1.5eba4300 62.745 51 19 0 566 616 29 79 2.49e-12 74.7
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1 54.181 299 130 6 1367 1664 210 502 6.45e-94 337
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1 58.333 72 25 1 1885 1956 787 853 2.98e-13 77.8
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PredGene_adi2mcaRNA27872_R0.t1 62.745 51 19 0 566 616 29 79 2.51e-12 74.7
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PASA_asmbl_610753.p1 55.556 180 78 2 1370 1549 211 388 1.70e-62 221
TET1 sp|Q3URK3|TET1_MOUSE Montipora_capitata_PASA_asmbl_610753.p1 62.745 51 19 0 566 616 29 79 1.35e-11 70.5
Make Pact blastdb
/Applications/ncbi-blast-2.6.0+/bin/makeblastdb -in /Users/hputnam/MyProjects/Holobiont_Integration/RAnalysis/Data/Transcriptomics/Pacuta_holotranscriptome_data_v1/Pocillopora_acuta_v1_gene_models_coding.pep.faa -dbtype prot
Blast Uniprot proteins against all Pact coding gene models
/Applications/ncbi-blast-2.6.0+/bin/blastp -query /Users/hputnam/MyProjects/Mcap_Genome/Mcap_Genome_Files/DNMTs_TET.fa \
-db Pocillopora_acuta_v1_gene_models_coding.pep.faa \
-outfmt 6 \
-max_target_seqs 10 \
-evalue 1e-05 \
-out Pact_DNMT_TET_hits_10
Pact Results
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00029688.p1 48.086 653 296 7 286 907 78 718 0.0 620
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00029687.p1 48.086 653 296 7 286 907 78 718 0.0 620
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00029686.p1 48.086 653 296 7 286 907 63 703 0.0 618
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00029689.p2 35.395 291 153 4 286 552 63 342 1.49e-51 185
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PASA_asmbl_153011.p1 68.889 90 26 1 737 824 1 90 5.37e-33 125
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PASA_asmbl_153009.p1 61.224 98 31 2 772 862 10 107 4.55e-30 115
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00029685.p2 35.583 163 79 3 286 424 78 238 2.10e-26 111
sp|Q1LZ53|DNM3A_RAT Pocillopora_acuta_PredGene_TCONS_00025917.p1 49.153 59 30 0 286 344 1308 1366 4.95e-12 71.2
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045317.p1 58.783 1446 528 19 123 1518 42 1469 0.0 1654
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045319.p1 54.821 1255 501 18 123 1328 42 1279 0.0 1295
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045320.p1 48.579 739 323 15 123 821 42 763 0.0 657
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045318.p1 48.579 739 323 15 123 821 42 763 0.0 657
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045316.p1 48.579 739 323 15 123 821 42 763 0.0 657
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00045321.p1 49.141 582 246 12 123 671 42 606 4.02e-170 526
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PASA_asmbl_232676.p1 40.000 110 57 3 745 845 5 114 4.16e-16 76.6
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00030544.p1 58.333 48 18 1 561 606 595 642 1.36e-10 67.4
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00030543.p2 58.333 48 18 1 561 606 595 642 1.57e-10 67.0
sp|Q92072|DNMT1_CHICK Pocillopora_acuta_PredGene_TCONS_00030542.p2 58.333 48 18 1 561 606 595 642 1.57e-10 67.0
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PredGene_TCONS_00033908.p1 52.381 315 139 5 1354 1664 193 500 2.30e-98 350
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PredGene_TCONS_00033908.p1 57.971 69 29 0 1884 1952 783 851 5.04e-14 79.3
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PredGene_TCONS_00033908.p1 61.224 49 19 0 565 613 28 76 1.25e-12 74.7
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PASA_asmbl_174291.p1 56.725 171 69 2 1494 1664 6 171 1.36e-56 216
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PASA_asmbl_174291.p1 57.971 69 29 0 1884 1952 454 522 3.34e-14 79.7
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PASA_asmbl_174290.p1 56.725 171 69 2 1494 1664 6 171 1.36e-56 216
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PASA_asmbl_174290.p1 57.971 69 29 0 1884 1952 454 522 3.34e-14 79.7
sp|Q3URK3|TET1_MOUSE Pocillopora_acuta_PASA_asmbl_174293.p1 57.971 69 29 0 1884 1952 274 342 1.72e-14 80.5
Written on July 28, 2020