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: CP000509.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
-------- ----------- ----- ------- ---
CP000509_0988 CDS_1070611-1071789 78.8 7.3e-23 1
CP000509_3592 CDS_3864123-3866015 63.6 2.1e-18 1
CP000509_2587 CDS_2803972-2805276 62.8 3.7e-18 1
CP000509_0919 CDS_996520-994910 57.3 1.5e-16 1
CP000509_3437 CDS_3696842-3698122 57.2 1.7e-16 1
CP000509_1283 CDS_1392354-1391200 55.0 7.1e-16 2
CP000509_3071 CDS_3322426-3324033 54.0 1.5e-15 1
CP000509_2894 CDS_3125268-3123811 49.5 3.1e-14 1
CP000509_0965 CDS_1043105-1044838 48.0 8.7e-14 1
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP000509_0988 1/1 190 257 .. 1 70 [] 78.8 7.3e-23
CP000509_3592 1/1 442 494 .. 1 55 [. 63.6 2.1e-18
CP000509_2587 1/1 239 305 .. 1 70 [] 62.8 3.7e-18
CP000509_0919 1/1 344 409 .. 1 70 [] 57.3 1.5e-16
CP000509_3437 1/1 218 278 .. 1 63 [. 57.2 1.7e-16
CP000509_3071 1/1 327 392 .. 1 70 [] 54.0 1.5e-15
CP000509_1283 2/2 184 251 .. 1 70 [] 53.5 2e-15
CP000509_2894 1/1 273 339 .. 1 70 [] 49.5 3.1e-14
CP000509_0965 1/1 387 452 .. 1 70 [] 48.0 8.7e-14
Alignments of top-scoring domains:
CP000509_0988: domain 1 of 1, from 190 to 257: score 78.8, E = 7.3e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIARELHD+v+++ s++ lq++++r+++ + ++e real+++
CP000509_0 190 ERGRIARELHDVVAHAVSVMVLQVGAVRHRM--SDSDAENREALENV 234
relarealaevRrllgdLRpaal<-*
++++r alae+Rrllg++R +++
CP000509_0 235 ERAGRAALAEMRRLLGAMRRDGE 257
CP000509_3592: domain 1 of 1, from 442 to 494: score 63.6, E = 2.1e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER R+ARE+HD +g+sL++++lq+++arrl ++dpe+ar+al+++
CP000509_3 442 ERLRLAREIHDHIGHSLTVAALQAGAARRLG--TADPERARAALRTV 486
relareal<-*
+++are+l
CP000509_3 487 AAAAREGL 494
CP000509_2587: domain 1 of 1, from 239 to 305: score 62.8, E = 3.7e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe...eareal
ER+RIAR+LHD+v Q L++ + ++++ ++pe+++ ar++l
CP000509_2 239 ERRRIARDLHDTVVQDLAGTAYAISAL------SRNPEtptDARDTL 279
deirelarealaevRrllgdLRpaal<-*
d + +r++l+ +R ll +++p++l
CP000509_2 280 DGAGSSLRDGLKSLRSLLVEIHPPEL 305
CP000509_0919: domain 1 of 1, from 344 to 409: score 57.3, E = 1.5e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R+RIAR+LHD v Q+L+a lql++a ++ +++ e+++++de+
CP000509_0 344 DRERIARDLHDLVIQRLFATGLQLQGAGSMA--TSP--ELAARIDEA 386
relarealaevRrllgdLRpaal<-*
+++ +++++R ++ +L++ ++
CP000509_0 387 VVALDMTIKDIRGTIFELQHRGH 409
CP000509_3437: domain 1 of 1, from 218 to 278: score 57.2, E = 1.7e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
aR+AR+ HD+vg+sL++i q+e a+ l d+d + +++++d+i
CP000509_3 218 DQARLARDVHDVVGHSLAVILAQAESAQFLR--DADTGTLQRTMDNI 262
relarealaevRrllg<-*
+++are+l++vR++l+
CP000509_3 263 ATTARESLDDVRQVLS 278
CP000509_3071: domain 1 of 1, from 327 to 392: score 54.0, E = 1.5e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe..eareald
ER+R+ARE+HD+++Q ++++ ++++ ++dp++++ +++++
CP000509_3 327 ERRRLAREIHDGLAQDIASLGYLVDAL------AADPGtpAQAARIA 367
eirelarealaevRrllgdLRpaal<-*
+re ++ +evR+ + +LR+++
CP000509_3 368 GLRERISAVVTEVRDSVVTLRTGVG 392
CP000509_1283: domain 2 of 2, from 184 to 251: score 53.5, E = 2e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIARE+HD++++++s i++++++++ + d ++e r ++ i
CP000509_1 184 EQARIAREMHDVLAHRISQISMHAGALAFRD--DLTADEMRSSAAVI 228
relarealaevRrllgdLRpaal<-*
+e a+eal+++R +lg+LR++a
CP000509_1 229 QEKAHEALTDLRGVLGVLRDDAT 251
CP000509_2894: domain 1 of 1, from 273 to 339: score 49.5, E = 3.1e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +ARELHD Q+L+ ++ l+ + +++ +++p e++ +l +
CP000509_2 273 ERRALARELHDDPLQNLTYLSRALDDLGHRA--ETPP-ELAGQLVDA 316
relarealaevRrllgdLRpaal<-*
+ a++a +R ++++LRp++l
CP000509_2 317 SAVAEDAAVALRKVIHGLRPPVL 339
CP000509_0965: domain 1 of 1, from 387 to 452: score 48.0, E = 8.7e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RI R+LHD v Q+L+a+ l l+ +r++ ++ e+ + ld++
CP000509_0 387 DRDRIGRDLHDLVIQRLFAVGLSLQSSARAA--GSP--ELTAKLDAA 429
relarealaevRrllgdLRpaal<-*
+ ++++++++Rr++ +L a+
CP000509_0 430 VDDLDTTIRDIRRTIFALGSAEN 452
Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-14 3 0|=
-13 22 0|==
-12 52 51|====*
-11 101 425|========= *
-10 382 987|================================ *
-9 687 1121|==========================================================*
-8 669 864|======================================================== *
-7 680 543|=============================================*===========
-6 604 307|=========================*=========================
-5 579 164|=============*===================================
-4 309 86|=======*==================
-3 196 44|===*=============
-2 142 22|=*==========
-1 83 11|*======
0 46 5|*===
1 30 2|*==
2 18 1|*=
3 12 0|=
4 6 0|=
5 0 0|
6 5 0|=
7 2 0|=
8 3 0|=
9 0 0|
10 1 0|=
11 0 0|
12 1 0|=
> 13 12 -|=
% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 4634.7397
P(chi-square) = 0
Total sequences searched: 4645
Whole sequence top hits:
tophits_s report:
Total hits: 9
Satisfying E cutoff: 9
Total memory: 21K
Domain top hits:
tophits_s report:
Total hits: 9
Satisfying E cutoff: 9
Total memory: 24K
