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Classification of phyla is from NCBI page
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4 accessions found for Rhodococcus erythropolis PR4  

Data for AP008957  

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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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/projects/MicrobialGenomicsGroup/Packages/hmmdata-1.0.0.package/Resources/noarch/TCS/HisKA_3.hmm [HisKA_3]
Sequence database: AP008957.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]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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
-------- ----------- ----- ------- ---
AP008957_3134 CDS_3400112-3398949 93.1 5.6e-27 1
AP008957_3681 CDS_4025624-4024422 90.9 2.5e-26 1
AP008957_2141 CDS_2334423-2335610 90.0 4.6e-26 1
AP008957_4711 CDS_5152017-5153141 85.6 8.8e-25 1
AP008957_2387 CDS_2577976-2579250 80.7 2.6e-23 1
AP008957_0655 CDS_733784-734974 80.0 3.9e-23 1
AP008957_5960 CDS_6434464-6433316 79.9 4.4e-23 1
AP008957_1134 CDS_1265496-1266752 74.1 2.3e-21 1
AP008957_2302 CDS_2490937-2492082 73.3 3.9e-21 1
AP008957_0099 CDS_119118-117916 70.8 2.1e-20 1
AP008957_1029 CDS_1149226-1150503 65.3 8.4e-19 1
AP008957_5419 CDS_5869201-5870385 58.2 1.1e-16 1
AP008957_1784 CDS_1918496-1919956 57.0 2.4e-16 1
AP008957_4465 CDS_4896953-4898644 52.4 5.7e-15 1
AP008957_2917 CDS_3129653-3128418 51.1 1.4e-14 1
AP008957_1230 CDS_1361395-1359695 47.6 1.4e-13 1
AP008957_3420 CDS_3745986-3744295 45.9 4.6e-13 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AP008957_3134 1/1 185 252 .. 1 70 [] 93.1 5.6e-27
AP008957_3681 1/1 190 257 .. 1 70 [] 90.9 2.5e-26
AP008957_2141 1/1 189 256 .. 1 70 [] 90.0 4.6e-26
AP008957_4711 1/1 191 258 .. 1 70 [] 85.6 8.8e-25
AP008957_2387 1/1 218 285 .. 1 70 [] 80.7 2.6e-23
AP008957_0655 1/1 195 262 .. 1 70 [] 80.0 3.9e-23
AP008957_5960 1/1 196 263 .. 1 70 [] 79.9 4.4e-23
AP008957_1134 1/1 222 289 .. 1 70 [] 74.1 2.3e-21
AP008957_2302 1/1 170 237 .. 1 70 [] 73.3 3.9e-21
AP008957_0099 1/1 200 265 .. 1 70 [] 70.8 2.1e-20
AP008957_1029 1/1 222 289 .. 1 70 [] 65.3 8.4e-19
AP008957_5419 1/1 193 260 .. 1 70 [] 58.2 1.1e-16
AP008957_1784 1/1 255 320 .. 1 70 [] 57.0 2.4e-16
AP008957_4465 1/1 358 424 .. 1 70 [] 52.4 5.7e-15
AP008957_2917 1/1 198 271 .. 1 70 [] 51.1 1.4e-14
AP008957_1230 1/1 362 428 .. 1 70 [] 47.6 1.4e-13
AP008957_3420 1/1 368 433 .. 1 70 [] 45.9 4.6e-13

Alignments of top-scoring domains:
AP008957_3134: domain 1 of 1, from 185 to 252: score 93.1, E = 5.6e-27
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD+v+++ s++++q+++a +++ d++p+ a++al +i
AP008957_3 185 ERTRIARELHDVVAHAVSVMIVQADGASYAV--DSNPALAKKALGNI 229

relarealaevRrllgdLRpaal<-*
++r+alae+Rr+++ LR+ +
AP008957_3 230 SSTGRDALAELRRTVSLLRTEVS 252

AP008957_3681: domain 1 of 1, from 190 to 257: score 90.9, E = 2.5e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIAR+LHD+v++++++++lq+++a +l+ kdpe+a +al+ +
AP008957_3 190 ERMRIARDLHDVVAHHIALVNLQVGVASHLI--GKDPEKATTALRGV 234

relarealaevRrllgdLRpaal<-*
+e+++ al+e+R+++g+LR+a++
AP008957_3 235 EETSKAALDEIRATVGVLRDAQD 257

AP008957_2141: domain 1 of 1, from 189 to 256: score 90.0, E = 4.6e-26
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER RIARE+HD v++sL++++ q+++ r+ + +kdp++a +al++i
AP008957_2 189 ERSRIAREMHDIVAHSLTVVIAQADGGRYSA--AKDPQAAIQALETI 233

relarealaevRrllgdLRpaal<-*
+ ++r+al+++R ll++LR+++
AP008957_2 234 ASTGRQALTDMRSLLSVLREDTP 256

AP008957_4711: domain 1 of 1, from 191 to 258: score 85.6, E = 8.8e-25
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+AR+LHD +g+sL++i++++ela rll d d e+ar +ld +
AP008957_4 191 ERTRMARDLHDILGHSLTVITIKAELANRLL--DVDIERARNELDDL 235

relarealaevRrllgdLRpaal<-*
++l+r+ala+vR ++ ++R l
AP008957_4 236 ERLSRDALADVRSAVEGFRGISL 258

AP008957_2387: domain 1 of 1, from 218 to 285: score 80.7, E = 2.6e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E aRIAR+LHD v++++s++ +q++ a ++l d+ +e+r++++ i
AP008957_2 218 EKARIARDLHDIVAHHMSMVVVQAQSAPYRL--DAVTPEIRTEFESI 262

relarealaevRrllgdLRpaal<-*
e++r al+e+R llg+LR +++
AP008957_2 263 SETGRAALNEIRGLLGVLRSDGD 285

AP008957_0655: domain 1 of 1, from 195 to 262: score 80.0, E = 3.9e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIAR++HD+++ sLs i+l +++++ + +++pe++ ++++i
AP008957_0 195 ERTRIARDMHDTIAASLSRISLFAGGLQVSA--ADNPEKVVNTAAMI 239

relarealaevRrllgdLRpaal<-*
r++a+eal+e+ ++g+LR +++
AP008957_0 240 RTTAHEALDELKGIVGVLRGSGD 262

AP008957_5960: domain 1 of 1, from 196 to 263: score 79.9, E = 4.4e-23
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER R +R+LHD+vg +Lsai++++ela++l ++ +++a++++de+
AP008957_5 196 ERLRFSRDLHDVVGRALSAIAVKSELAATLS--RRGDDRAAAQMDEV 240

relarealaevRrllgdLRpaal<-*
rela+++l+e+R+l++++R al
AP008957_5 241 RELAQDSLDEARELVRGYRSIAL 263

AP008957_1134: domain 1 of 1, from 222 to 289: score 74.1, E = 2.3e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
E +RI R+LHD+ +L a+ ++l++a+r l + +p++a +l+++
AP008957_1 222 ELKRIERDLHDGAQNRLVAVVMMLGMAERSL--QNNPDQALPQLHRA 266

relarealaevRrllgdLRpaal<-*
+++a eal+e+R l++d+ p++l
AP008957_1 267 QDAATEALSELRTLVHDIYPPIL 289

AP008957_2302: domain 1 of 1, from 170 to 237: score 73.3, E = 3.9e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER +ARELHD v++++++i l +++a+++l + +e++re l+ +
AP008957_2 170 ERSALARELHDLVAHHMASIVLRIGVAQHVL--APQDEAVREVLADV 214

relarealaevRrllgdLRpaal<-*
r++a++ala++Rrll +LR++ l
AP008957_2 215 RATASDALADIRRLLVALRDPSL 237

AP008957_0099: domain 1 of 1, from 200 to 265: score 70.8, E = 2.1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe.earealde
ER+R+A E+HD+v+Q+Ls+i + l++a+ ++dpe++a +++
AP008957_0 200 ERERLAAEIHDTVAQGLSSIQMLLHAAE-----RADPEsPAIRQISL 241

irelarealaevRrllgdLRpaal<-*
+re+a ++lae+R+l+ +L paal
AP008957_0 242 ARETAADSLAETRQLIAELTPAAL 265

AP008957_1029: domain 1 of 1, from 222 to 289: score 65.3, E = 8.4e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +ARELHD+ +++++++++q+ +a + + ++pe+a++ l +
AP008957_1 222 ERQDMARELHDVAAHHMTGMIIQARAADKFF--SSNPEQAQALLGGV 266

relarealaevRrllgdLRpaal<-*
e +++al+ +R+++g LR +++
AP008957_1 267 IEQGQRALNSLRQIVGILRLGEE 289

AP008957_5419: domain 1 of 1, from 193 to 260: score 58.2, E = 1.1e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+R+ARE+HD+v Q+L+++ l le+a++ + + r+ +d++
AP008957_5 193 ERERLAREIHDTVTQGLASALLRLEAAEQTW--NTTGSPSRADVDAA 237

relarealaevRrllgdLRpaal<-*
+e +r++l + R+l++dL pa
AP008957_5 238 AENIRTSLMQSRDLVHDLAPAKG 260

AP008957_1784: domain 1 of 1, from 255 to 320: score 57.0, E = 2.4e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHDsv Q+ ++ +q+e++r + +++ e e+ld +
AP008957_1 255 ERHRIARELHDSVTQAVLSAGMQIEVCRSDI--PEA--ERSERLDLA 297

relarealaevRrllgdLRpaal<-*
++l r+a +++R ++ +L ++ +
AP008957_1 298 KDLTRRAVEQLRSAIYALNHSSD 320

AP008957_4465: domain 1 of 1, from 358 to 424: score 52.4, E = 5.7e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrllds.dkdpeearealde
R RIAR+LHD v Q+L+a + l+ + ++++ pe ar+ +++
AP008957_4 358 DRDRIARDLHDNVIQRLFASGMSLQSTL----PdETLPESARAIVKR 400

irelarealaevRrllgdLRpaal<-*
e ++++ +e+R ++ dL++++
AP008957_4 401 SLEQLDKTVREIRTTIFDLQTPTA 424

AP008957_2917: domain 1 of 1, from 198 to 271: score 51.1, E = 1.4e-14
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpe......ear
ERa +AR+LHD+++ +Lsai++++e+a+ + e++++++ +r
AP008957_2 198 ERATMARDLHDVIASHLSAIAIHSEAALSTS--ALSGErgepddGLR 242

ealdeirelarealaevRrllgdLRpaal<-*
e + +ir + +l+e+R ++ L+ +++
AP008957_2 243 EMIGAIRSSSLAGLSEMRSMIELLHAGDD 271

AP008957_1230: domain 1 of 1, from 362 to 428: score 47.6, E = 1.4e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIAR+LHD v Q+L+a l l++a+ + + d e +r+ ld+
AP008957_1 362 DRDRIARDLHDHVIQQLFATGLSLQGAL-QR--PGDEETIRTVLDNS 405

relarealaevRrllgdLRpaal<-*
+ ++++ +e+R ++ dL++++
AP008957_1 406 VDQLDRTVREIRTAVFDLHTSEM 428

AP008957_3420: domain 1 of 1, from 368 to 433: score 45.9, E = 4.6e-13
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
R RIAR+LHD v Q+++a+ l +++ ++++ +++ e+ ++l
AP008957_3 368 DRDRIARDLHDHVIQRIFAVGLSVQGTLQRT--RAP--EVHQRLSGT 410

relarealaevRrllgdLRpaal<-*
+ +++ ++++Rr++ dL+ +++
AP008957_3 411 IDDLQDIIQDIRRAIFDLHATED 433


Histogram of all scores:
score obs exp (one = represents 19 sequences)
----- --- ---
-14 5 0|=
-13 60 0|====
-12 142 67|===*====
-11 220 553|============ *
-10 686 1283|===================================== *
-9 1090 1457|==========================================================*
-8 1017 1123|====================================================== *
-7 853 706|=====================================*=======
-6 626 399|====================*============
-5 585 214|===========*===================
-4 286 111|=====*==========
-3 182 57|==*=======
-2 103 29|=*====
-1 67 14|*===
0 36 7|*=
1 20 3|*=
2 12 1|*
3 10 0|=
4 3 0|=
5 5 0|=
6 2 0|=
7 2 0|=
8 1 0|=
9 0 0|
10 0 0|
11 1 0|=
12 1 0|=
> 13 19 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 2474.6567
P(chi-square) = 0

Total sequences searched: 6034

Whole sequence top hits:
tophits_s report:
Total hits: 17
Satisfying E cutoff: 17
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 17
Satisfying E cutoff: 17
Total memory: 26K


Acknowledgements:

This research is funded by:

Developed by: