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Other Bacteria Planctomycetes Spirochaetes
Thermotogae
Classification of phyla is from NCBI page
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35 projects found  

1 accessions found for Syntrophobacter fumaroxidans MPOB  

Data for CP000478  

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: CP000478.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
-------- ----------- ----- ------- ---
CP000478_3634 CDS_4479212-4477260 64.9 7.7e-19 1
CP000478_2365 CDS_2949441-2947834 58.6 5.4e-17 1
CP000478_3223 CDS_3986193-3984508 49.1 3.6e-14 1
CP000478_1850 CDS_2285486-2287147 48.5 5.3e-14 1
CP000478_3212 CDS_3971504-3973858 46.3 2.4e-13 1
CP000478_3180 CDS_3934691-3933507 36.2 2.3e-10 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000478_3634 1/1 449 515 .. 1 70 [] 64.9 7.7e-19
CP000478_2365 1/1 314 382 .. 1 70 [] 58.6 5.4e-17
CP000478_3223 1/1 347 415 .. 1 70 [] 49.1 3.6e-14
CP000478_1850 1/1 349 415 .. 1 70 [] 48.5 5.3e-14
CP000478_3212 1/1 568 636 .. 1 70 [] 46.3 2.4e-13
CP000478_3180 1/1 192 258 .. 1 70 [] 36.2 2.3e-10

Alignments of top-scoring domains:
CP000478_3634: domain 1 of 1, from 449 to 515: score 64.9, E = 7.7e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD++g sLs ik le+ +r++ + + e l+++
CP000478_3 449 ERKRIARELHDGIGSSLSTIKFSLEATLRRM--RQGS-QSYESLQNV 492

relarealaevRrllgdLRpaal<-*
l ++a++e Rr+ +dLRp++l
CP000478_3 493 IVLTQHAIDESRRIMTDLRPPIL 515

CP000478_2365: domain 1 of 1, from 314 to 382: score 58.6, E = 5.4e-17
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHDs gQsL+a+k ++ a+ + + + p+e + ld++
CP000478_2 314 ERKRIARELHDSTGQSLAALKFYVDNALNMKE-RGKPDEMANCLDRM 359

relarealaevRrllgdLRpaal<-*
l+r a++e+Rr+ +LRp++l
CP000478_2 360 VPLIRNAIEEARRIYMGLRPSIL 382

CP000478_3223: domain 1 of 1, from 347 to 415: score 49.1, E = 3.6e-14
*->ERaRIARELHDsvgQsLsaiklqle.larrlldsdkdpeearealde
ERaR+A ELHDs+gQ+L a+k ++e++++ ++ +++ + ld
CP000478_3 347 ERARLAHELHDSIGQTLVAVKFGIEnALKGRT--VGGLDAVSQLLDP 391

irelarealaevRrllgdLRpaal<-*
+ +++ a +e+R l +LRp++l
CP000478_3 392 LVPMVQNAVEEARKLYMGLRPTIL 415

CP000478_1850: domain 1 of 1, from 349 to 415: score 48.5, E = 5.3e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHDs+g +Lsaik l ++ +k e++ ++
CP000478_1 349 ERRRIARELHDSIGSALSAIKFSLANTMEQM--RKGK-TDPETFVTL 392

relarealaevRrllgdLRpaal<-*
+ + + a++e Rrl +dLRp++l
CP000478_1 393 MNMTQNAIDESRRLMTDLRPSIL 415

CP000478_3212: domain 1 of 1, from 568 to 636: score 46.3, E = 2.4e-13
*->ERaRIARELHDsvgQsLsaiklqle.larrlldsdkdpeearealde
ER+R A ELHDs+gQsL+aik ++e+++r+ + + e + l
CP000478_3 568 ERKRVAAELHDSIGQSLAAIKYGVEnAVRYGA--SAGEETVFHSLGL 612

irelarealaevRrllgdLRpaal<-*
+ +++ a++e+Rrl +LRp+ l
CP000478_3 613 LIPIIQGAIEEARRLYMGLRPSML 636

CP000478_3180: domain 1 of 1, from 192 to 258: score 36.2, E = 2.3e-10
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA E HDs+g +L+aik le + + kd++++ eal++
CP000478_3 192 ERKRIALEVHDSIGSTLTAIKFSLEHIVSEA---KDAPAVCEALKTP 235

relarealaevRrllgdLRpaal<-*
+ a++e R + dLRpa+l
CP000478_3 236 ISFTQIAIEESRKIMNDLRPAVL 258


Histogram of all scores:
score obs exp (one = represents 13 sequences)
----- --- ---
-14 8 0|=
-13 58 0|=====
-12 97 45|===*====
-11 166 372|============= *
-10 511 864|======================================== *
-9 744 981|==========================================================*
-8 624 756|================================================ *
-7 574 475|====================================*========
-6 408 269|====================*===========
-5 401 144|===========*===================
-4 172 75|=====*========
-3 117 38|==*======
-2 75 19|=*====
-1 45 10|*===
0 31 5|*==
1 12 2|*
2 6 1|*
3 5 0|=
4 2 0|=
> 5 8 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 1633.7463
P(chi-square) = 0

Total sequences searched: 4064

Whole sequence top hits:
tophits_s report:
Total hits: 6
Satisfying E cutoff: 6
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 6
Satisfying E cutoff: 6
Total memory: 22K


Acknowledgements:

This research is funded by:

Developed by: