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Classification of phyla is from NCBI page
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106 projects found  

3 accessions found for Nocardia farcinica IFM 10152  

Data for AP006618  

Available Atlases
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hmmsearch - search a sequence database with a profile HMM
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: AP006618.Gprot.fsa
per-sequence score cutoff: >= 30.1 [TC1]
per-domain score cutoff: >= 30.1 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA_3
Accession: PF07730.2
Description: Histidine kinase
[HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
AP006618_3128 CDS_3319962-3318784 88.8 9.9e-26 1
AP006618_4261 CDS_4408666-4407329 83.4 3.7e-24 1
AP006618_0785 CDS_851947-850898 82.3 8.3e-24 1
AP006618_0419 CDS_438696-437491 80.5 2.7e-23 1
AP006618_3041 CDS_3223839-3222733 68.2 1.1e-19 1
AP006618_4254 CDS_4398844-4397534 62.9 4.2e-18 1
AP006618_0422 CDS_442139-440640 62.5 5.4e-18 1
AP006618_2241 CDS_2414450-2415826 50.9 1.5e-14 1
AP006618_2899 CDS_3078905-3077154 48.5 7.4e-14 1
AP006618_2293 CDS_2464373-2465743 39.8 2.8e-11 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AP006618_3128 1/1 182 249 .. 1 70 [] 88.8 9.9e-26
AP006618_4261 1/1 203 271 .. 1 70 [] 83.4 3.7e-24
AP006618_0785 1/1 153 217 .. 1 70 [] 82.3 8.3e-24
AP006618_0419 1/1 183 251 .. 1 70 [] 80.5 2.7e-23
AP006618_3041 1/1 170 237 .. 1 70 [] 68.2 1.1e-19
AP006618_4254 1/1 222 291 .. 1 70 [] 62.9 4.2e-18
AP006618_0422 1/1 186 253 .. 1 70 [] 62.5 5.4e-18
AP006618_2241 1/1 236 307 .. 1 70 [] 50.9 1.5e-14
AP006618_2899 1/1 390 455 .. 1 70 [] 48.5 7.4e-14
AP006618_2293 1/1 259 325 .. 1 70 [] 39.8 2.8e-11

Alignments of top-scoring domains:
AP006618_3128: domain 1 of 1, from 182 to 249: score 88.8, E = 9.9e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD+v+++ s+i++q+++ar++l ++dp++a++al i
AP006618_3 182 ERTRIARELHDVVAHAVSVIIVQADGARYAL--RRDPDAAEQALGVI 226

relarealaevRrllgdLRpaal<-*
++++real+e+Rr++ LR+
AP006618_3 227 AGTGREALRELRRTVALLRTEHA 249

AP006618_4261: domain 1 of 1, from 203 to 271: score 83.4, E = 3.7e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIAR+LHD+v++++s++ +q+++a +++ + +e+ar++++ i
AP006618_4 203 EKARIARDLHDVVAHHMSLVVVQAQTAPYRV--AGVNEAARAEFESI 247

relarealaevRrllgdLR.paal<-*
++areal+e+R +lg+LR++++
AP006618_4 248 STTAREALNEIRGMLGVLRsDGVA 271

AP006618_0785: domain 1 of 1, from 153 to 217: score 82.3, E = 8.3e-24
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD++gQsL+++ l + +a dk+p++a e+l+ +
AP006618_0 153 ERRRIARELHDEIGQSLTVALLSMKRAI-----DKAPGPAGEELRGA 194

relarealaevRrllgdLRpaal<-*
+e++r +l+evR ++++LRp++l
AP006618_0 195 QETVRACLDEVRGIARRLRPDVL 217

AP006618_0419: domain 1 of 1, from 183 to 251: score 80.5, E = 2.7e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER IARELHD++++sLs+i++q+++a++l+ d++pe+ar al++i
AP006618_0 183 ERLSIARELHDVLAHSLSLINVQSSVALALF--DAEPEQARSALAAI 227

relarealaevRrllgdLR.paal<-*
+++++++laev ll ++R a l
AP006618_0 228 KTASKDSLAEVHTLLETIRaGAPL 251

AP006618_3041: domain 1 of 1, from 170 to 237: score 68.2, E = 1.1e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER +IARELHDs+ + +s+ik+q+e+a +++ +k ee+ +al +i
AP006618_3 170 ERLHIARELHDSLTHEISVIKVQSEAAVHVA--RKRGEEVPAALLAI 214

relarealaevRrllgdLRpaal<-*
r+++rea +e+R++l +LR++++
AP006618_3 215 RDAGREAARELRATLEALRDDGE 237

AP006618_4254: domain 1 of 1, from 222 to 291: score 62.9, E = 4.2e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrllds.dkdpeearealde
ER+RIARE HD++++sLs+ l+l +ar++l ++d+d +ea +al
AP006618_4 222 ERRRIAREVHDVIAHSLSVTLLHLTAARHAL-QtDRDVDEAVDALVD 267

irelarealaevRrllgdLRpaal<-*
+++l+r+a+a++Rr++g L + +
AP006618_4 268 AERLGRQAMADIRRTVGLLGERTA 291

AP006618_0422: domain 1 of 1, from 186 to 253: score 62.5, E = 5.4e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER ARELHD++++sLs+i++q+++a+ l+ ++ p +ar al++i
AP006618_0 186 ERLTAARELHDVLAHSLSLINVQSSVALELF--ERKPMQARSALAAI 230

relarealaevRrllgdLRpaal<-*
+++++++l+ev +ll ++R + +
AP006618_0 231 KKASKDSLDEVHALLPTIRRGPF 253

AP006618_2241: domain 1 of 1, from 236 to 307: score 50.9, E = 1.5e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ER+RIARELHDsv Q ++ + +e +r l + p+ ++e+ e l
AP006618_2 236 ERHRIARELHDSVTQDVLSAGMTIEICRSEL--AGTPGvddEIVEKL 280

deirelarealaevRrllgdLR.paal<-*
++r+l r+a + +R+++ +L+++a++
AP006618_2 281 SAARDLTRHAVERLRAAIYALHrTADE 307

AP006618_2899: domain 1 of 1, from 390 to 455: score 48.5, E = 7.4e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIAR+LHD v Q+L+a+ l l+ ++ +++ e++++l
AP006618_2 390 ERDRIARDLHDHVIQRLFAVGLSLQSTVSRA--RAP--EIKTRLMDT 432

relarealaevRrllgdLRpaal<-*
++ +e+R+ + dL+ +
AP006618_2 433 VNDVQSIVQEIRHSIFDLHSSSA 455

AP006618_2293: domain 1 of 1, from 259 to 325: score 39.8, E = 2.8e-11
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
+R R+LHD+ +L i++ l++a+ ++ ++++ ar+ ++
AP006618_2 259 TLRRVERDLHDGTQARLVTIAMALGRAE-----ERLAAggDARDLIA 300

eirelarealaevRrllgdLRpaal<-*
+++ ++eal+e+R+l+++++p+al
AP006618_2 301 DAHASSKEALTELRELVRGIHPPAL 325


Histogram of all scores:
score obs exp (one = represents 14 sequences)
----- --- ---
-14 3 0|=
-13 49 0|====
-12 92 63|====*==
-11 174 520|============= *
-10 509 1208|===================================== *
-9 799 1372|==========================================================*
-8 782 1057|======================================================== *
-7 808 664|===============================================*==========
-6 689 376|==========================*=======================
-5 725 201|==============*=====================================
-4 366 105|=======*===================
-3 263 54|===*===============
-2 154 27|=*=========
-1 103 14|*=======
0 60 7|*====
1 40 3|*==
2 15 1|*=
3 17 0|==
4 8 0|=
5 7 0|=
6 2 0|=
7 1 0|=
8 1 0|=
9 1 0|=
> 10 15 -|==


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 5581.5537
P(chi-square) = 0

Total sequences searched: 5683

Whole sequence top hits:
tophits_s report:
Total hits: 10
Satisfying E cutoff: 10
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 10
Satisfying E cutoff: 10
Total memory: 24K


Acknowledgements:

This research is funded by:

Developed by: