Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate HSERO_RS14940 HSERO_RS14940 aconitate hydratase
Query= BRENDA::A0A090AMG4
(901 letters)
>FitnessBrowser__HerbieS:HSERO_RS14940
Length = 903
Score = 1436 bits (3717), Expect = 0.0
Identities = 720/905 (79%), Positives = 797/905 (88%), Gaps = 6/905 (0%)
Query: 1 MPHNTLDTLKNFKI-GNKSCQYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVT 59
M NTL+TLK FKI G+K ++YSLPAL KSLG+++ RLPVSIRIVLESVLRNCDG+KVT
Sbjct: 1 MSRNTLNTLKEFKISGSKKGKFYSLPALQKSLGVNISRLPVSIRIVLESVLRNCDGQKVT 60
Query: 60 EEHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEP 119
EEHVKQLANW A A R DEIPFVVARVVLQDFTGVPLLAD+AAMR+VA K+GK+PK+IEP
Sbjct: 61 EEHVKQLANWGAKAARVDEIPFVVARVVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEP 120
Query: 120 LVPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGI 179
LVPVDLVVDHSV ID+F K ALDLNMKLEF RN ERYQFMKWGMQAFDTFGVVPPGFGI
Sbjct: 121 LVPVDLVVDHSVQIDHFREKKALDLNMKLEFSRNNERYQFMKWGMQAFDTFGVVPPGFGI 180
Query: 180 VHQVNLEYLARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 239
VHQVNLEYLARGVH K VYYPD+LVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP
Sbjct: 181 VHQVNLEYLARGVH--NKTGVYYPDTLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQP 238
Query: 240 VYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERA 299
VYFLTPDVVGV L G LR GVTATDLVLTITE+LR+ KVVGKFVEF GEGT SLS+ +RA
Sbjct: 239 VYFLTPDVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFGEGTESLSLTDRA 298
Query: 300 TIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFT 359
TI NMAPEYGATMGFFPVD+ TI+YF+GTGRT+AEI AFEAYFKAQ+++GVPKA I++T
Sbjct: 299 TIANMAPEYGATMGFFPVDDATIEYFKGTGRTKAEIDAFEAYFKAQELYGVPKAGQIDYT 358
Query: 360 KLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS 419
+ ++LDL TVAPSLAGPKRPQDRIEIGNVK+TF DL++KP AENGFN+ AE L ++ +
Sbjct: 359 QEVSLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAEDLGASYKNA 418
Query: 420 AGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVT 479
G + NGD+LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGL V HIKTSLAPGSRVVT
Sbjct: 419 DGVDLHNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVT 478
Query: 480 EYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFE 539
+YL GLLPYLEKLGF V AYGCTTCIGNAGDLTP +NEAI+ ND++ +AVLSGNRNFE
Sbjct: 479 KYLEAAGLLPYLEKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAAVLSGNRNFE 538
Query: 540 ARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIESL 598
ARIHPNI+ANFLASPPLVVAYA+AG VTRDLMTEPVG+GK G D++LGDIWPT++EIE L
Sbjct: 539 ARIHPNIRANFLASPPLVVAYAIAGNVTRDLMTEPVGKGKGGKDIYLGDIWPTSQEIEKL 598
Query: 599 LKYALDPKAFEANYGQVKSNPGKLWENTKGVT-GDTYNWPDSTYIAEPPFFEGFGMTPGA 657
LK+A++ K F+ NY VK PGKLWE KGV G+ YNWP STYIAEPPFFE F P A
Sbjct: 599 LKFAMNAKTFKENYADVKGAPGKLWEAIKGVAKGEVYNWPSSTYIAEPPFFENFSEEPKA 658
Query: 658 MPA-VKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHE 716
A + GARALGVFGDS+TTDHISPAGSIKE+SPAGKWL+ NGV+KADFNSYGSRRGNHE
Sbjct: 659 AAAGITGARALGVFGDSITTDHISPAGSIKESSPAGKWLQANGVLKADFNSYGSRRGNHE 718
Query: 717 IMMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFG 776
IMMRGTFANVRIKNLMIPA DGSR EGG T+ QP+GE+MSIYDAAMKYV+ GTPT+VFG
Sbjct: 719 IMMRGTFANVRIKNLMIPAKEDGSRVEGGITIHQPSGEEMSIYDAAMKYVAEGTPTMVFG 778
Query: 777 GEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGIT 836
GEEYGTGSSRDWAAKGTQLLGVKAVI RSFERIHRSNLVGMGVLPLQF G DSVQSLGIT
Sbjct: 779 GEEYGTGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFLGNDSVQSLGIT 838
Query: 837 GEETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLR 896
G+ET+D+ GLE IKP Q+ TL I RK+G ++V +LLRIDTPIEVDYY+HGGILPFVLR
Sbjct: 839 GDETFDLKGLEGEIKPQQEATLVIHRKNGETKEVKLLLRIDTPIEVDYYKHGGILPFVLR 898
Query: 897 QLLAA 901
QLLAA
Sbjct: 899 QLLAA 903
Lambda K H
0.317 0.136 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2397
Number of extensions: 99
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 901
Length of database: 903
Length adjustment: 43
Effective length of query: 858
Effective length of database: 860
Effective search space: 737880
Effective search space used: 737880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate HSERO_RS14940 HSERO_RS14940 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR01341.hmm
# target sequence database: /tmp/gapView.31736.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01341 [M=876]
Accession: TIGR01341
Description: aconitase_1: aconitate hydratase 1
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1294.1 0.0 0 1293.9 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS14940 HSERO_RS14940 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14940 HSERO_RS14940 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1293.9 0.0 0 0 2 876 .] 19 901 .. 18 901 .. 0.97
Alignments for each domain:
== domain 1 score: 1293.9 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkpar 68
k ++ysl+al++s + +is+lp s+ri+lesvlrn+dg+k++ee+v++l++w +++ + ei+f +ar
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 19 KGKFYSLPALQKSlGVNISRLPVSIRIVLESVLRNCDGQKVTEEHVKQLANWGAKAARVDEIPFVVAR 86
6789********9788**************************************************** PP
TIGR01341 69 vvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefern 136
vvlqdftGvp++ dlaa+r+ ++lgk+p+ i+plvpvdlv+dhsvq+d+++e++al+ n++lef rn
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 87 VVLQDFTGVPLLADLAAMRNVASKLGKNPKNIEPLVPVDLVVDHSVQIDHFREKKALDLNMKLEFSRN 154
******************************************************************** PP
TIGR01341 137 kerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGl 204
+ery+f+kw+ +af + vvppg Givhqvnleyla+ v++++ + ypd+lvGtdshttminG+
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 155 NERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHNKT----GVYYPDTLVGTDSHTTMINGI 218
****************************************998....899****************** PP
TIGR01341 205 GvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffG 272
Gv+GwGvGGieaea++lGqpv++ p+v+Gv+ltG lreGvtatdlvlt+tellr+ vvgkfveffG
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 219 GVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVNLTGALREGVTATDLVLTITELLRQTKVVGKFVEFFG 286
******************************************************************** PP
TIGR01341 273 eglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dsee 339
eg ++lsl+dratianmapeyGat++ffp+dd t++y++ tgr + +++ e+y kaqel+ ++ +
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 287 EGTESLSLTDRATIANMAPEYGATMGFFPVDDATIEYFKGTGRTKAEIDAFEAYFKAQELYGVpKAGQ 354
*************************************************************988999* PP
TIGR01341 340 pkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakek.klegkeae 406
+ yt+ v ldl +v +s+aGpkrpqdr+++ +vk++f + ++++e+g++ + e + +
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 355 IDYTQEVSLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFTKPTAENGFNKKAEDLGAsYKNADGVD 422
*************************************************987755543303378999* PP
TIGR01341 407 lkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyl 474
l++g+v iaaitsctntsnpsvll+agllakkave+Glkv p++ktslapGs+vvt+yl +gllpyl
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 423 LHNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVAPHIKTSLAPGSRVVTKYLEAAGLLPYL 490
******************************************************************** PP
TIGR01341 475 eelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvva 542
e+lGf + yGcttciGn+G+l+ +++eai++nd++++avlsGnrnfe+rihp ++an+laspplvva
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 491 EKLGFGVTAYGCTTCIGNAGDLTPAMNEAIVKNDVVAAAVLSGNRNFEARIHPNIRANFLASPPLVVA 558
******************************************************************** PP
TIGR01341 543 yalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevteg.nerwnel 609
ya+aG+v+ dl +ep+g +k Gk++yl diwp+ +ei++l k a++ + fk++y+ v++ + w+ +
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 559 YAIAGNVTRDLMTEPVGKGKGGKDIYLGDIWPTSQEIEKLLKFAMNAKTFKENYADVKGApGKLWEAI 626
*********************************************************9763689**** PP
TIGR01341 610 e.vtssdlyewdekstyireppffeelklepeeved.ikgarillllGdsittdhispaGsikkdspa 675
+ v+++++y+w + styi eppffe+++ ep+ i+gar l ++GdsittdhispaGsik+ spa
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 627 KgVAKGEVYNW-PSSTYIAEPPFFENFSEEPKAAAAgITGARALGVFGDSITTDHISPAGSIKESSPA 693
86899******.68*****************986544******************************* PP
TIGR01341 676 akylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvy 737
+k+l+ +Gv + dfnsyGsrrGnhe+m+rGtfan+rikn ++++k eGg+t++ p +e++s+y
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 694 GKWLQANGVLKADFNSYGSRRGNHEIMMRGTFANVRIKNLMIPAKedgsrvEGGITIHQPSGEEMSIY 761
******************************************97533333369*************** PP
TIGR01341 738 daamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqg 805
daamky eg+p++v G+eyG+Gssrdwaakgt+llGvkavia+sferihrsnlvgmGvlpl+f
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 762 DAAMKYVAEGTPTMVFGGEEYGTGSSRDWAAKGTQLLGVKAVIARSFERIHRSNLVGMGVLPLQFLGN 829
******************************************************************** PP
TIGR01341 806 edaetlgltgeetidvddie.elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvl 872
++ ++lg+tg+et d++++e e+kp++e+t+++ +++ge + v+ lridt++e++y+k+gGil +vl
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 830 DSVQSLGITGDETFDLKGLEgEIKPQQEATLVIHRKNGETKEVKLLLRIDTPIEVDYYKHGGILPFVL 897
******************8549********************************************** PP
TIGR01341 873 rkll 876
r+ll
lcl|FitnessBrowser__HerbieS:HSERO_RS14940 898 RQLL 901
*986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (903 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 11.20
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory