HMM profiles of Arabidopsis NBS domain based on the
alignment
were generated using hmmbuild and
hmmemit programs.
----------------------------------------------------
Based on total alignment:
>NBS_712 profile HMM generated consensus sequence [hmmemit]
dfedlVGieahlkkleslLcldsddeVrmiGIwGmgGIGKTTLAraLynq
lssqFdlscFvenskefsveqrpigldelgmqeqlLskilnqkdieienh
lgvlkerLkdkKVLlVLDDVdkleqLdaLaketpWfGpGSRIIiTTrDks
lLkahginhiYeVkcLseeeAlqLFcryAFgqksppdgfeeLskvevvkl
cgGLPLALkVlGssLrgKgskeeWedalprLetsldgenIesvLkvSYDg
LdeedKdcFLyiAcFFniekedlVkylLaeggeldgrvglkvLvdksLit
isddgrveMHdLlremgreiaseegcrpgkrqfLvdapeicdvltnrtgt
sVlGIsLDslsinkieliisekafkrMrnLrfLkiyssh
We have analyzed non-redundant NCBI protein database and Arabidopsis MIPS database with this HMM Arabidopsis NBS profile using hmmsearch program and results of search you may find here:
nr NCBI database: NBS_HMM_NCBI.search
MIPS protein database: NBS_HMM_MIPS.search
----------------------------------------------------
Based on the alignment of non-TIR sequences:
>NBS_SubDomA profile HMM generated consensus sequence [hmmemit]
erpsestiVGletmleklwnrLledndvgivgiyGMGGVGKTTLatqifN
dfdvkgehFdrviWVvVSkefnvekiqqdIlekLglgdeewlekteeeka
aeienLfqlLegKkfLLvLDDvWekevdLdkigvpfPdrenGsKvlfTTR
sesvavcgdmgvdxmevecLtpeeAWeLFqkkvfentlksdpeieelaKe
vvkkCgGLPLAlkVlGgllacKrtvqEWkraievlssslaaefsgmessi
lpvLklSYdnLppelKsCFLYcalFPEDykIekekLieyWiaEGfidese
ggetaedvGyeylgeLVrrsLleegdktdnetsrketVkMHDvvREmALw
iaseegfkeviiVraGvglreipnvkswntvrRmSlmnneieelldspen
pklrsLltlllqsnsh
hmmsearch search against:
nr NCBI database: NBS_SubA_HMM_NCBI.search
MIPS protein database: NBS_SubA_HMM_MIPS.search
----------------------------------------------------
Based on the alignment of TIR-containing sequences:
>NBS_SubDomB profile HMM generated consensus sequence [hmmemit]
rDFddlVGiEaHlekmksLLcLdsdeVrMVGIwGPaGIGKTTIARALfsq
LSssFqlsaFmenlrgsyStrpaglDeYsmKLhLQeqfLSkILnqkDikI
hHLGvieERLkdqKVLIiLDDVDdleQLdALAketqWFGpGSRIIVTTeD
kqLLkaHgInhIYeVgfPSkeeALqIFCrsAFgQnsPpdGFeeLAreVtk
LaGnLPLGLrVlGSsLRGkskeeWedmLpRLrtsLDgkIekvLrvsYDgL
hekDqaLFLhIACfFNgekvdyVkalLadsnLDVrqGLkvLadKSLIhis
plgdgtieMHnLLqqLGReIVrkQsidePgKRqFLvDaeeIcdVLtdnTG
tgsVlGIslDtseieeelnIsekAFegMrNLqFLriykksfrddgk
hmmsearch search against:
nr NCBI database: NBS_SubB_HMM_NCBI.search
MIPS protein database: NBS_SubB_HMM_MIPS.search
----------------------------------------------------
