CDD注释[Ubuntu系统]

使用网页工具：

CD-search:http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

使用RPS-BLAST将protein序列或者nucleotide序列比对到CDD数据库的PSSMs，得到注释结果。此工具一次只能搜索到一条序列。

结果如下：

#Batch CD-search tool	NIH/NLM/NCBI
#cdsid	QM3-qcdsearch-6A273CE59470C7A-27758A4251131776
#datatype	hitsConcise Results
#status	0
#Start time	2016-06-03T14:59:15	Run time	0:00:00:12
#status	success

Query	                     Hit type	PSSM-ID	From	To	E-Value	Bitscore	Accession	Short name	Incomplete	Superfamily
Q#1 - >At1g01220_1	specific	249743	819	877	2.51156e-10	56.0224	pfam00288	GHMP_kinases_N	 - 	cl21671
Q#1 - >At1g01220_1	superfamily	272091	819	877	2.51156e-10	56.0224	cl21671	GHMP_kinases_N superfamily	 - 	 - 
Q#1 - >At1g01220_1	specific	254869	962	1043	2.94031e-07	47.8594	pfam08544	GHMP_kinases_C	 - 	cl08484
Q#1 - >At1g01220_1	superfamily	254869	962	1043	2.94031e-07	47.8594	cl08484	GHMP_kinases_C superfamily	 - 	 - 
Q#1 - >At1g01220_1	multi-dom	254543	131	531	0	563.303	pfam07959	Fucokinase	 - 	 - 
Q#1 - >At1g01220_1	multi-dom	225325	718	1048	5.17247e-41	152.917	COG2605	COG2605	 - 	 - 
Q#2 - >At1g01220_2	superfamily	252914	1	82	8.30867e-23	87.0152	cl04867	LRAT superfamily	N	 - 
Q#3 - >At1g01350_1	specific	238093	277	318	2.90528e-09	50.9072	cd00162	RING	 - 	cl17238
Q#3 - >At1g01350_1	superfamily	276201	277	318	2.90528e-09	50.9072	cl17238	RING superfamily	 - 	 - 
Q#3 - >At1g01350_1	specific	250023	201	227	4.96868e-07	44.0832	pfam00642	zf-CCCH	 - 	cl11592
Q#3 - >At1g01350_1	superfamily	264437	201	227	4.96868e-07	44.0832	cl11592	zf-CCCH superfamily	 - 	 - 
Q#4 - >At1g01350_2	specific	199896	2	147	8.00992e-62	188.701	cd10910	limkain_b1_N_like	 - 	cl10034
Q#4 - >At1g01350_2	superfamily	275915	2	147	8.00992e-62	188.701	cl10034	LabA_like/DUF88 superfamily	 - 	 - 

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Batch CD-Search

http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi

那能一次性比对多条protein序列（多达100，00条每次）

同时提供网页工具和脚本接口。

比对完毕后，可以下载注释结果。

序列：

>At1g01220_1
MSKQRKKADLATVLRKSWYHLRLSVRHPTRVPTWDAIVLTAASPEQAELYDWQLRRAKRMGRIASSTVTL
AVPDPDGKRIGSGAATLNAIYALARHYEKLGFDLGPEMEVANGACKWVRFISAKHVLMLHAGGDSKRVPW
ANPMGKVFLPLPYLAADDPDGPVPLLFDHILAIASCARQAFQDQGGLFIMTGDVLPCFDAFKMTLPEDAA
SIVTVPITLDIASNHGVIVTSKSESLAESYTVSLVNDLLQKPTVEDLVKKDAILHDGRTLLDTGIISARG
RAWSDLVALGCSCQPMILELIGSKKEMSLYEDLVAAWVPSRHDWLRTRPLGELLVNSLGRQKMYSYCTYD
LQFLHFGTSSEVLDHLSGDASGIVGRRHLCSIPATTVSDIAASSVILSSEIAPGVSIGEDSLIYDSTVSG
AVQIGSQSIVVGIHIPSEDLGTPESFRFMLPDRHCLWEVPLVGHKGRVIVYCGLHDNPKNSIHKDGTFCG
KPLEKVLFDLGIEESDLWSSYVAQDRCLWNAKLFPILTYSEMLKLASWLMGLDDSRNKEKIKLWRSSQRV
SLEELHGSINFPEMCNGSSNHQADLAGGIAKACMNYGMLGRNLSQLCHEILQKESLGLEICKNFLDQCPK
FQEQNSKILPKSRAYQVEVDLLRACGDEAKAIELEHKVWGAVAEETASAVRYGFREHLLESSGKSHSENH
ISHPDRVFQPRRTKVELPVRVDFVGGWSDTPPWSLERAGYVLNMAITLEGSLPIGTIIETTNQMGISIQD
DAGNELHIEDPISIKTPFEVNDPFRLVKSALLVTGIVQENFVDSTGLAIKTWANVPRGSGLGTSSILAAA
VVKGLLQISNGDESNENIARLVLVLEQLMGTGGGWQDQIGGLYPGIKFTSSFPGIPMRLQVVPLLASPQL
ISELEQRLLVVFTGQVRLAHQVLHKVVTRYLQRDNLLISSIKRLTELAKSGREALMNCEVDEVGDIMSEA
WRLHQELDPYCSNEFVDKLFEFSQPYSSGFKLVGAGGGGFSLILAKDAEKAKELRQRLEEHAEFDVKVYN
WSIFQRPPSCEVTVLPLPGIKVKRPRKISTLVAFGFGDNAVKRLCNGQPDS
>At1g01220_2
GVVLSCLDCFLKNGSLYCFEYGVSPSVFLTKVRGGTCTTAQSDTTDSVIHRAMYLLQNGFGNYDIFKNNC
EDFALYCKTGLLIMDKLGVGRSGQASSIVGAPLAALLSSPFKLLIPSPIGVATVTAGMYCMSRYATDIGV
RSDVIKVSVEDLALNLDVKTIEQGEEEEEDEEEDSDTDYVR
>At1g01350_1
MSDSGEPKPSQQEEPLPQPAAQETQSQQVCTFFKKPTKSKNIRKRTIDADEEDGDSKSESSILQNLKKVA
KPDSKLYFSSGPSKSSTTTSGAPERSVFHYDSSKEIQVQNDSGATATLETETDFNQDARAIRERVLKKAD
EALKGNKKKASDEKLYKGIHGYTDHKAGFRREQTISSEKAGGSHGPLRASAHIRVSARFDYQPDICKDYK
ETGYCGYGDSCKFLHDRGDYKPGWQIEKEWEEAEKVRKRNKAMGVEDEDDEADKDSDEDENALPFACFIC
REPFVDPVVTKCKHYFCEHCALKHHTKNKKCFVCNQPTMGIFNAAHEIKKRMAEERSKAEQGLRRLWPVG
EVVPKSK
>At1g01350_2
AVTRVWWDINRCPVPADVDVRRVGPCIKRALEKLGYSGPLTITAVGILTDVPHDFLRQVHSSGIALHHVP
TVSETALSGIGWAVVKWTWYNQPPANLMLISYEHIYLTTLDMLGRIGYNTVRSILPDDPQQAASSASPST
GSFLWESLLASLPAADDMDSGAPQEDKCGEMGEPALLCEQCRFTVQGFENFSTHLKSEEHAHESQYYRNE
DDETDGDDYVRDSEDDEEE
>At1g01660_1
MAELMAMGNDVVHVAVKSDVRESRSTLLWALRNLGAKKVCILHVYQPKTASPAARKLEELEAIMYETLHD
YFDFCQQEGVNEDDIYISCIEMNDVKQGILELIHESKIKKLVMGAASDHHYSEKMFDLKSRKAKYVYQHA
PSSCEVMFMCDGHLIYTKEANLEDCMGETESEAGQSKPKLYSSASPKCSAELVSAIVAYIDTRRDRDMLE
PNASEDQSESDRNDQLYRQLKQALMEVEESKREAYEECVRRFKAENTAVEAIRSAREYEAMYNEEAKLRK
EGKEALAKQRKMVEKTKQERDDALIIILNGRKLYNEELRRRVEAEEMLGKEKEEHERTKKEIEEVRAIVQ
DGTLYNEQLRHRKEMEESMKRQEEELEKTKKEKEEACMISKNLMQLYEDEVRQRKEAEELVKRRREELEK
VKKEKEEACSVGQNFMRLYEEEARRRKGTEEELSKVAAEKDAASSVCSEILLLLQSYTRRHGTPSGFSDE
DSVTRQPP
>At1g01660_2
SYFICPISQEVMREPRVAADGFTYEAESLREWLDNGHETSPMTNLKLAHNNLVPNHALRSAIQEWLQRNS
>At1g02230_1
MMNPVGFRFRPNDEEIVDHYLRPKNLDSDTSHVDEVISTVDICSFEPWDLPSKSMIKSRDGVWYFFSVKE
MKYNRGDQQRRRTNSGFWKKTGKTMTVMRKRGNREKIGEKRVLVFKNRDGSKTDWVMHEYHATSLFPNQM
MTYTVCKVEFKGEETEISSSSTGSEIEQIHSLIPLVNSSGGSEVGESQTFSVLSLETLKYLTLVFLPFFR
GESQIDDATTPIEEEWKTWLNNDGDEQRNIMFMQDHRSDYTPLKSLTGVFSDDSSDDNDSDLISPKTNSI
GTSSTCASFASSNHQIDQTQHSPDSTVQLVSLTQEVSQGPGQVTVIREHKLGEESVKKKRASFVYRMIHR
LVKKIHQC

结果：

#Batch CD-search tool	NIH/NLM/NCBI
#cdsid	QM3-qcdsearch-1C0005B737A3865C-39D60DE8A7221C8D
#datatype	hitsConcise Results
#status	0
#Start time	2016-06-04T01:48:41	Run time	0:00:00:14
#status	success

Query	                        Hit type	PSSM-ID	From	To	E-Value	Bitscore	Accession	Short name	Incomplete	Superfamily
Q#1 - >At1g01220_1	specific	249743	819	877	2.51156e-10	56.0224	pfam00288	GHMP_kinases_N	 - 	cl21671
Q#1 - >At1g01220_1	superfamily	272091	819	877	2.51156e-10	56.0224	cl21671	GHMP_kinases_N superfamily	 - 	 - 
Q#1 - >At1g01220_1	specific	254869	962	1043	2.94031e-07	47.8594	pfam08544	GHMP_kinases_C	 - 	cl08484
Q#1 - >At1g01220_1	superfamily	254869	962	1043	2.94031e-07	47.8594	cl08484	GHMP_kinases_C superfamily	 - 	 - 
Q#1 - >At1g01220_1	multi-dom	254543	131	531	0	563.303	pfam07959	Fucokinase	 - 	 - 
Q#1 - >At1g01220_1	multi-dom	225325	718	1048	5.17247e-41	152.917	COG2605	COG2605	 - 	 - 
Q#2 - >At1g01220_2	superfamily	252914	1	82	8.30867e-23	87.0152	cl04867	LRAT superfamily	N	 - 
Q#3 - >At1g01350_1	specific	238093	277	318	2.90528e-09	50.9072	cd00162	RING	 - 	cl17238
Q#3 - >At1g01350_1	superfamily	276201	277	318	2.90528e-09	50.9072	cl17238	RING superfamily	 - 	 - 
Q#3 - >At1g01350_1	specific	250023	201	227	4.96868e-07	44.0832	pfam00642	zf-CCCH	 - 	cl11592
Q#3 - >At1g01350_1	superfamily	264437	201	227	4.96868e-07	44.0832	cl11592	zf-CCCH superfamily	 - 	 - 
Q#4 - >At1g01350_2	specific	199896	2	147	8.00992e-62	188.701	cd10910	limkain_b1_N_like	 - 	cl10034
Q#4 - >At1g01350_2	superfamily	275915	2	147	8.00992e-62	188.701	cl10034	LabA_like/DUF88 superfamily	 - 	 - 
Q#5 - >At1g01660_1	specific	238947	11	152	1.00963e-46	157.823	cd01989	STK_N	 - 	cl00292
Q#5 - >At1g01660_1	superfamily	275515	11	152	1.00963e-46	157.823	cl00292	AANH_like superfamily	 - 	 - 
Q#6 - >At1g01660_2	specific	128780	2	65	5.29778e-30	98.8465	smart00504	Ubox	 - 	cl17238
Q#6 - >At1g01660_2	superfamily	276201	2	65	5.29778e-30	98.8465	cl17238	RING superfamily	 - 	 - 
Q#7 - >At1g02230_1	specific	251251	4	133	2.83212e-63	196.656	pfam02365	NAM	 - 	cl03558
Q#7 - >At1g02230_1	superfamily	251251	4	133	2.83212e-63	196.656	cl03558	NAM superfamily	 - 	 - 

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