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Classification of phyla is from NCBI page
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106 projects found  

1 accessions found for Thermobifida fusca YX  

Data for CP000088  

Available Atlases
Other Plots
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: CP000088.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
-------- ----------- ----- ------- ---
CP000088_0287 CDS_327841-326570 90.7 1.5e-26 1
CP000088_0766 CDS_911403-910216 89.5 3.3e-26 1
CP000088_1839 CDS_2153981-2152731 74.5 8.7e-22 2
CP000088_2225 CDS_2628961-2630088 74.1 1.1e-21 1
CP000088_1400 CDS_1625742-1626965 72.0 4.9e-21 1
CP000088_0327 CDS_370304-371611 71.3 7.5e-21 1
CP000088_2270 CDS_2681815-2683026 65.3 4.6e-19 1
CP000088_3039 CDS_3561570-3563288 43.5 1.2e-12 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000088_0287 1/1 219 286 .. 1 70 [] 90.7 1.5e-26
CP000088_0766 1/1 198 265 .. 1 70 [] 89.5 3.3e-26
CP000088_1839 2/2 206 272 .. 1 70 [] 74.5 8.8e-22
CP000088_2225 1/1 175 243 .. 1 70 [] 74.1 1.1e-21
CP000088_1400 1/1 197 264 .. 1 70 [] 72.0 4.9e-21
CP000088_0327 1/1 241 308 .. 1 70 [] 71.3 7.5e-21
CP000088_2270 1/1 197 265 .. 1 70 [] 65.3 4.6e-19
CP000088_3039 1/1 377 442 .. 1 70 [] 43.5 1.2e-12

Alignments of top-scoring domains:
CP000088_0287: domain 1 of 1, from 219 to 286: score 90.7, E = 1.5e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER R AR++HD +g+sLs+i++++ela+rl+ ++dpe+a+++++e+
CP000088_0 219 ERLRFARDMHDLLGHSLSGIAVKSELAARLA--RSDPERAAAEMAEV 263

relarealaevRrllgdLRpaal<-*
+++areal+evR++++++R l
CP000088_0 264 QRIAREALREVRAAVSGYRAVNL 286

CP000088_0766: domain 1 of 1, from 198 to 265: score 89.5, E = 3.3e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER ARE HD++++++s+i++q++ a++l+ d+ pe+a+eal++i
CP000088_0 198 ERLKFAREVHDVIAHNISLINVQAGSALYLI--DTQPERAAEALAAI 242

relarealaevRrllgdLRpaal<-*
++++re+l+e+R++lg+LR ++
CP000088_0 243 KQASRETLQELRAILGVLRAVDE 265

CP000088_1839: domain 2 of 2, from 206 to 272: score 74.5, E = 8.8e-22
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARE+HD+v+++ s++ l++++++ + +++ + +e ++ i
CP000088_1 206 ERTRIAREMHDVVAHRVSLMVLHAGGLEVSA--PDE--RTAEIAELI 248

relarealaevRrllgdLR.paal<-*
r+++real+e+R++lg+LR+ a
CP000088_1 249 RTTGREALSELREILGVLRnGEAA 272

CP000088_2225: domain 1 of 1, from 175 to 243: score 74.1, E = 1.1e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+ IARE+HD++g++Ls++++++++++++ d++p+ +++a++ i
CP000088_2 175 AREEIAREIHDVLGHRLSLLSVHAGALAYRP--DAPPQDIARAARVI 219

relarealaevRrllgdLR.paal<-*
re a++al+++R+++g+LR p ++
CP000088_2 220 RESAHQALQDLRQVVGVLRaPVGE 243

CP000088_1400: domain 1 of 1, from 197 to 264: score 72.0, E = 4.9e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERaR+ARELHD+v+ +Lsa++lq+ +a++l + dpe++r l+++
CP000088_1 197 ERARMARELHDVVANHLSAVALQSTAALALR--EFDPERVRGVLRTV 241

relarealaevRrllgdLRpaal<-*
r+ + ++lae+Rr++ +LR ++
CP000088_1 242 RDNSVRGLAEMRRMIEVLRAGEQ 264

CP000088_0327: domain 1 of 1, from 241 to 308: score 71.3, E = 7.5e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RI R+LHD+ Q+L +++l l +ar+ + d+dpe+are ++e+
CP000088_0 241 ERRRIERDLHDGAQQRLLSLTLTLARARAKF--DRDPEQARELVEEA 285

relarealaevRrllgdLRpaal<-*
++ ar +ae+R+++++L+p +l
CP000088_0 286 QREARAVMAELREVARGLHPKVL 308

CP000088_2270: domain 1 of 1, from 197 to 265: score 65.3, E = 4.6e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERaR+AR++HDsv+ +L +++l ++++ l +kdpe+a+++++++
CP000088_2 197 ERARLARDMHDSVAKTLHGAALAAQALPVWL--RKDPERAEATAAQV 241

relarealaevRrllgdLR.paal<-*
++a++a +e+R+l++dLR+++ +
CP000088_2 242 VKAAETAAREARQLISDLReETSD 265

CP000088_3039: domain 1 of 1, from 377 to 442: score 43.5, E = 1.2e-12
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIA +LHD+v Q+L+ai++ l r++ ++d ++++++++
CP000088_3 377 DRDRIAKDLHDVVIQRLFAIAMSLMSSVRRI--EDD--TVAQRIQQA 419

relarealaevRrllgdLRpaal<-*
+ ++++++++R ++ +L++ ++
CP000088_3 420 VDDLDDTIRQIRSTIFALQHNTE 442


Histogram of all scores:
score obs exp (one = represents 8 sequences)
----- --- ---
-14 2 0|=
-13 15 0|==
-12 47 34|====*=
-11 76 285|========== *
-10 263 661|================================= *
-9 448 751|======================================================== *
-8 415 578|==================================================== *
-7 462 363|=============================================*============
-6 386 205|=========================*=======================
-5 400 110|=============*====================================
-4 202 57|=======*==================
-3 132 29|===*=============
-2 94 15|=*==========
-1 53 7|*======
0 29 3|*===
1 31 1|*===
2 12 1|*=
3 17 0|===
4 3 0|=
5 3 0|=
6 6 0|=
7 1 0|=
8 0 0|
9 2 0|=
10 0 0|
11 0 0|
12 1 0|=
> 13 10 -|==


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2899.2834
P(chi-square) = 0

Total sequences searched: 3110

Whole sequence top hits:
tophits_s report:
Total hits: 8
Satisfying E cutoff: 8
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 8
Satisfying E cutoff: 8
Total memory: 23K


Acknowledgements:

This research is funded by:

Developed by: