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Classification of phyla is from NCBI page
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1 accessions found for Leptothrix cholodnii SP-6  

Data for CP001013  

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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: CP001013.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
-------- ----------- ----- ------- ---
CP001013_0898 CDS_967674-966145 73.3 2.8e-21 1
CP001013_1774 CDS_1928091-1926586 71.3 1.1e-20 1
CP001013_1393 CDS_1488505-1489659 67.2 1.8e-19 1
CP001013_2408 CDS_2626274-2627416 63.0 3e-18 1
CP001013_1587 CDS_1693991-1692834 54.9 7.2e-16 1
CP001013_3827 CDS_4316408-4317901 52.5 3.7e-15 1
CP001013_0242 CDS_262557-261085 32.9 2.2e-09 1

Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
CP001013_0898 1/1 290 355 .. 1 70 [] 73.3 2.8e-21
CP001013_1774 1/1 268 335 .. 1 70 [] 71.3 1.1e-20
CP001013_1393 1/1 169 234 .. 1 70 [] 67.2 1.8e-19
CP001013_2408 1/1 47 114 .. 1 70 [] 63.0 3e-18
CP001013_1587 1/1 162 227 .. 1 70 [] 54.9 7.2e-16
CP001013_3827 1/1 252 318 .. 1 70 [] 52.5 3.7e-15
CP001013_0242 1/1 278 345 .. 1 70 [] 32.9 2.2e-09

Alignments of top-scoring domains:
CP001013_0898: domain 1 of 1, from 290 to 355: score 73.3, E = 2.8e-21
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIARELHD++gQ+L+a+k+ l+++++ + +++l+ +
CP001013_0 290 ERRRIARELHDELGQRLTALKMDLSGLAA----ANGLKDTDKHLAGM 332

relarealaevRrllgdLRpaal<-*
++++e+ a vRr++gdLRp l
CP001013_0 333 LTMLDETVASVRRIAGDLRPLML 355

CP001013_1774: domain 1 of 1, from 268 to 335: score 71.3, E = 1.1e-20
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa+++RELHD+ gQ+L +ikl ++ a +l +++ ++ +ld +
CP001013_1 268 ERAHLSRELHDGTGQTLVSIKLLMDSAIGHL--KRNLQAPPPTLDKA 312

relarealaevRrllgdLRpaal<-*
re ++eal+evR l ++LRp++l
CP001013_1 313 RERIDEALSEVRTLSHRLRPTVL 335

CP001013_1393: domain 1 of 1, from 169 to 234: score 67.2, E = 1.8e-19
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ IARE+HD++gQ L+++k+ + +++r + d++++r d++
CP001013_1 169 ERTAIAREIHDELGQVLTVLKMDIAWLAR----HPDDARLRVKTDAM 211

relarealaevRrllgdLRpaal<-*
+l++++++ vR + +LRp +l
CP001013_1 212 SRLIDDTIRSVRKISAGLRPEVL 234

CP001013_2408: domain 1 of 1, from 47 to 114: score 63.0, E = 3e-18
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+RIA ELHD + Q+L+ai l ++++r +l ++ + + ++ld++
CP001013_2 47 ERRRIASELHDDLQQTLAAIGLEVGAIRGQL--AAQACDLTARLDTV 91

relarealaevRrllgdLRpaal<-*
rela +a+a +Rr++ dLRp++l
CP001013_2 92 RELAITAIAATRRIVNDLRPPIL 114

CP001013_1587: domain 1 of 1, from 162 to 227: score 54.9, E = 7.2e-16
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ I+RE+HD vg sL+a+k l ++ r ++ +++ e+++++
CP001013_1 162 ERTAISREIHDDVGGSLTAVKFDLAWIVR----HAGNAQMIERAQQA 204

relarealaevRrllgdLRpaal<-*
e++++a++ r+ ++LRpa+l
CP001013_1 205 LETVNHAIEASQRIMHNLRPAIL 227

CP001013_3827: domain 1 of 1, from 252 to 318: score 52.5, E = 3.7e-15
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ERa +ARELHD+ gQ+L+a++ + ++ r+l ++ p e+ + ++ +
CP001013_3 252 ERALLARELHDEFGQRLTALRFDAAWLVRRL--ADQP-ELCAVAQGM 295

relarealaevRrllgdLRpaal<-*
+e + e ++++R+ll +LRp +
CP001013_3 296 AERCGEVQRDIRDLLVRLRPLGP 318

CP001013_0242: domain 1 of 1, from 278 to 345: score 32.9, E = 2.2e-09
*->ERaRIARELHDsvgQsLsaiklqlelarrlldsdkdpeearealdei
ER+ +ARELHD++gQs +ai+ + + ++l + +++ re ++ i
CP001013_0 278 ERREMARELHDELGQSVTAIRSVANSLVHRL--GERDAAGREMAALI 322

relarealaevRrllgdLRpaal<-*
a + ++ + l+ +L p al
CP001013_0 323 SSEAARLYEVMHGLIPRLTPLAL 345


Histogram of all scores:
score obs exp (one = represents 12 sequences)
----- --- ---
-14 7 0|=
-13 33 0|===
-12 73 48|===*===
-11 147 399|============= *
-10 443 927|===================================== *
-9 668 1053|======================================================== *
-8 600 812|================================================== *
-7 597 510|==========================================*=======
-6 542 288|=======================*======================
-5 467 154|============*==========================
-4 272 80|======*================
-3 185 41|===*============
-2 138 21|=*==========
-1 58 10|*====
0 43 5|*===
1 34 2|*==
2 12 1|*
3 10 0|=
4 10 0|=
5 4 0|=
6 1 0|=
7 2 0|=
8 1 0|=
9 1 0|=
10 3 0|=
11 2 0|=
> 12 10 -|=


% Statistical details of theoretical EVD fit:
mu = -8.7900
lambda = 0.6787
chi-sq statistic = 3534.0947
P(chi-square) = 0

Total sequences searched: 4363

Whole sequence top hits:
tophits_s report:
Total hits: 7
Satisfying E cutoff: 7
Total memory: 21K

Domain top hits:
tophits_s report:
Total hits: 7
Satisfying E cutoff: 7
Total memory: 23K


Acknowledgements:

This research is funded by:

Developed by: