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_1.hmm [HisKA]
Sequence database: AP011156.Gprot.fsa
per-sequence score cutoff: >= 26.8 [TC1]
per-domain score cutoff: >= 26.8 [TC2]
per-sequence Eval cutoff: [none]
per-domain Eval cutoff: [none]
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Query HMM: HisKA
Accession: PF00512.12
Description: His Kinase A (phosphoacceptor) domain
[HMM has been calibrated; E-values are empirical estimates]
Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
AP011156_0312 CDS_332005-333312 77.0 1.1e-21 1
AP011156_2287 CDS_2529129-2532446 74.6 5.5e-21 1
AP011156_0281 CDS_299967-298165 70.6 7.3e-20 1
AP011156_0154 CDS_176465-172983 69.3 1.7e-19 1
AP011156_1571 CDS_1721047-1719695 54.2 3.3e-15 1
AP011156_1722 CDS_1896459-1895350 53.5 5.1e-15 1
AP011156_0080 CDS_84597-86840 50.6 3.5e-14 1
AP011156_1720 CDS_1893841-1891577 50.0 5.2e-14 1
AP011156_1675 CDS_1847615-1846233 45.2 1.2e-12 1
AP011156_1013 CDS_1070977-1072977 41.6 1.2e-11 1
AP011156_0908 CDS_954498-955892 39.2 5.7e-11 1
AP011156_1012 CDS_1069143-1070993 26.9 1.8e-07 2
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AP011156_0312 1/1 178 245 .. 1 87 [] 77.0 1.1e-21
AP011156_2287 1/1 658 724 .. 1 87 [] 74.6 5.5e-21
AP011156_0281 1/1 365 430 .. 1 87 [] 70.6 7.3e-20
AP011156_0154 1/1 718 784 .. 1 87 [] 69.3 1.7e-19
AP011156_1571 1/1 223 289 .. 1 87 [] 54.2 3.3e-15
AP011156_1722 1/1 137 201 .. 1 87 [] 53.5 5.1e-15
AP011156_0080 1/1 350 418 .. 1 87 [] 50.6 3.5e-14
AP011156_1720 1/1 518 589 .. 1 87 [] 50.0 5.2e-14
AP011156_1675 1/1 253 320 .. 1 87 [] 45.2 1.2e-12
AP011156_1013 1/1 275 342 .. 1 87 [] 41.6 1.2e-11
AP011156_0908 1/1 232 299 .. 1 87 [] 39.2 5.7e-11
Alignments of top-scoring domains:
AP011156_0312: domain 1 of 1, from 178 to 245: score 77.0, E = 1.1e-21
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ ++f+a +sHELRTPL+a++g++e+L+ ++++++ ++
AP011156_0 178 QHTDFVAFASHELRTPLAALLGFIETLQG---------PAADDPVAQ 215
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+e+le++ ++a+r+++L+n lL lsr + +
AP011156_0 216 ----------KEFLEIMAQQAKRMQNLLNSLLYLSRVQMQ 245
AP011156_2287: domain 1 of 1, from 658 to 724: score 74.6, E = 5.5e-21
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
ak++ ++++sHE+R PL+aI+gy++lL+ dt ++ e
AP011156_2 658 AKTRYISGISHEIRSPLNAIMGYIQLLQH--------DTRMPTER-- 694
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
++ l++++++++++ ++++ lLd+srieag
AP011156_2 695 ----------QQTLSIMRESGDHITSILSGLLDISRIEAG 724
AP011156_0281: domain 1 of 1, from 365 to 430: score 70.6, E = 7.3e-20
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a ++f+a++sHE+++PL++Ir ++e+Ll+ e +q
AP011156_0 365 AIERFAADVSHEIKNPLSSIRSAIETLLR---------IEDLNQQ-- 400
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
r++l +i ++++rl+rLi d+ d sr++a+
AP011156_0 401 ----------RRLLTIINDDVRRLDRLITDISDASRLDAE 430
AP011156_0154: domain 1 of 1, from 718 to 784: score 69.3, E = 1.7e-19
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ks+f+ ++sHE+RTPL++I+gya lL++ l +e++
AP011156_0 718 SKSRFMVGVSHEIRTPLNSIMGYAYLLEN---------KMLAPEKQ- 754
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
e l++i+r+ae+l+ Li+ l d+s+ieag
AP011156_0 755 ----------NEGLKVIQRSAEHLSGLIEGLFDISKIEAG 784
AP011156_1571: domain 1 of 1, from 223 to 289: score 54.2, E = 3.3e-15
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ f+a+++HELR+PL a+++ +++L + l+e +
AP011156_1 223 TERAFAASAAHELRNPLGALLAQVQMLGR----------MLPEGSSA 259
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ +e+i + ++rl r ++ lL++sr+ +g
AP011156_1 260 ----------NKRVEIIADRTQRLARTVEKLLQFSRASSG 289
AP011156_1722: domain 1 of 1, from 137 to 201: score 53.5, E = 5.1e-15
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+ s ++a+l+HE R+PL++I+g+a+lL+ + ++ +
AP011156_1 137 SVSGLAAMLAHEVRNPLSGIKGAAQLLEQ----------AVTDAD-- 171
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
r++ i +e++r+++L++++ + ++
AP011156_1 172 ----------RDLATLICDEVDRIDALVDRMGMFGEAQLD 201
AP011156_0080: domain 1 of 1, from 350 to 418: score 50.6, E = 3.5e-14
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a+++f+a+++H++++ Lt+I+g++el+ e +d + eqr
AP011156_0 350 ALGQFTAGIAHDFKNLLTVILGNLELAAE-------HDLPDQVEQR- 388
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+eyl+ + + ++r ++L ++lL + r ++
AP011156_0 389 ----------QEYLSAATHVGHRSEALTSQLLSFMRRQQT 418
AP011156_1720: domain 1 of 1, from 518 to 589: score 50.0, E = 5.2e-14
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a + ++ ++HE+++PLt I+++ae L++++ +++ + ++++
AP011156_1 518 AWADVARRIAHEIKNPLTPIQLAAERLKRRF----LKEITSDPDT-- 558
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ + +ti r++ + r+++++ ++r+ ++
AP011156_1 559 ---------FSQCADTIVRQVGDIGRMVDEFSAFARMPQP 589
AP011156_1675: domain 1 of 1, from 253 to 320: score 45.2, E = 1.2e-12
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
+++ la++sH+LRTPLt +r+ ++++ + + +e++
AP011156_1 253 QRTGVLAGVSHDLRTPLTRLRLSLDMMPR--------TGMVRAEDI- 290
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ +e ++ ++ ++++i L ++r e
AP011156_1 291 ----------QPDVEDMIGDVAEMEHMIASYLAFARGEGT 320
AP011156_1013: domain 1 of 1, from 275 to 342: score 41.6, E = 1.2e-11
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
a + ++ +++H++++ LtaI+g +el ++ e + e
AP011156_1 275 AIGTLAGGIAHDFNNLLTAIQGSLELVQD---------LEPPREP-- 310
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+++++ + + ++a+r L + lLd+sr ++
AP011156_1 311 --------GVARLYQNAMEAARRGGTLTRKLLDFSRPRHL 342
AP011156_0908: domain 1 of 1, from 232 to 299: score 39.2, E = 5.7e-11
*->akseflanlsHELRTPLtaIrgyaelLleeldkvlagdtelseeqrl
++e +++H+LRTPL+ +r+ +e +l +++++ +
AP011156_0 232 DMREVGNDIAHDLRTPLSRMRARLERALS--------AGAADPAAL- 269
peLRledpeyreyletilreaerllrLindlLdlsrieag<-*
+ ++ ++ ++++++l +i lL ++ ie+
AP011156_0 270 ----------EAAVGRAVDDLDQCLGIITALLRIAEIENS 299
Histogram of all scores:
score obs exp (one = represents 9 sequences)
----- --- ---
-15 1 0|=
-14 7 0|=
-13 34 1|*===
-12 110 59|======*======
-11 254 311|============================= *
-10 429 577|================================================ *
-9 508 596|========================================================= *
-8 456 446|=================================================*=
-7 351 281|===============================*=======
-6 222 161|=================*=======
-5 114 88|=========*===
-4 56 47|=====*=
-3 32 25|==*=
-2 12 13|=*
-1 11 6|*=
0 7 3|*
1 5 1|*
2 2 0|=
3 0 0|
4 0 0|
> 5 14 -|==
% Statistical details of theoretical EVD fit:
mu = -8.9758
lambda = 0.6525
chi-sq statistic = 156.2213
P(chi-square) = 7.957e-28
Total sequences searched: 2625
Whole sequence top hits:
tophits_s report:
Total hits: 12
Satisfying E cutoff: 12
Total memory: 21K
Domain top hits:
tophits_s report:
Total hits: 11
Satisfying E cutoff: 11
Total memory: 25K
