Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate H281DRAFT_06606 H281DRAFT_06606 aconitase
Query= BRENDA::A0A090AMG4
(901 letters)
>FitnessBrowser__Burk376:H281DRAFT_06606
Length = 905
Score = 1429 bits (3700), Expect = 0.0
Identities = 718/906 (79%), Positives = 790/906 (87%), Gaps = 6/906 (0%)
Query: 1 MPHNTLDTLKNFKIGNKSCQYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVTE 60
M HN TLK F G+ ++YSLP LGK+L I + RLPVSIRIVLESVLRN DGKK+ E
Sbjct: 1 MAHNLHKTLKEFDSGSGKGKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAE 60
Query: 61 EHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPL 120
EH+ QLANW+ A R DEIPFVV+RVVLQDFTGVPLLADIAAMR VA ++GK+PKSIEPL
Sbjct: 61 EHITQLANWKPTAPRVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPL 120
Query: 121 VPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIV 180
VPVDLVVDHSV ID+F KNALDLNMKLEF+RN ERYQFMKWGMQAFDTF VVPPG GIV
Sbjct: 121 VPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIV 180
Query: 181 HQVNLEYLARGVH--LDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 238
HQVNLEYLARGVH + + VYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ
Sbjct: 181 HQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 240
Query: 239 PVYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAER 298
PVYFLTPDVVGV LKG+LR GVTATDLVLTITE+LR+EKVVGKFVEF GEGT SLS+ +R
Sbjct: 241 PVYFLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVGKFVEFFGEGTRSLSLPDR 300
Query: 299 ATIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINF 358
ATIGNMAPEYGATMGFFPVDE+TIDYF+GTGRT+AEI+AF+ YFKAQ +FG+PK DI+F
Sbjct: 301 ATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQNLFGIPKEGDIDF 360
Query: 359 TKLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTT 418
TK++TLDL TVAPSLAGPKRPQDRIEIGNVK+TF DL+SKPVAENGF + L +TT
Sbjct: 361 TKVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADLDAQYTT 420
Query: 419 SAGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVV 478
S G VKNGD+LIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTV HIKTSLAPGSR+V
Sbjct: 421 SNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480
Query: 479 TEYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNF 538
TEYLTKTGLLPYL+KLGF +AAYGCTTCIGNAGDLTP+LNEAI ND++ +AVLSGNRNF
Sbjct: 481 TEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNF 540
Query: 539 EARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIES 597
EARIHPNI+ANFLASPPLVVAYA+AG +TRDLMTEPVG+GK G DV+LGDIWPT++E+
Sbjct: 541 EARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVND 600
Query: 598 LLKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFF-EGFGMTPG 656
LLK+ALD AF NY + + G LW +G G Y+WP STYIAEPPFF F MTP
Sbjct: 601 LLKFALDADAFRKNYASL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFFGNDFSMTPA 659
Query: 657 -AMPAVKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNH 715
++ AVK ARALG+FGDSVTTDHISPAGSIKE SPAGKWLKENGV KADFNSYGSRRGNH
Sbjct: 660 DSIAAVKNARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGNH 719
Query: 716 EIMMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVF 775
++MMRGTFANVRIKNLMIPA DGSR EGG T+ QP+GEQ+SIYDAAMKY+ AGTPT+VF
Sbjct: 720 DVMMRGTFANVRIKNLMIPAKADGSRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIVF 779
Query: 776 GGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGI 835
GEEYGTGSSRDWAAKGTQLLGVKAV+ RSFERIHRSNLVGMGVLPLQFKG+DSVQSLGI
Sbjct: 780 AGEEYGTGSSRDWAAKGTQLLGVKAVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGI 839
Query: 836 TGEETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVL 895
TGEETYDI GL KP Q+VTL I KDGS++ V VLLRIDTPIEVDYY+HGGILPFVL
Sbjct: 840 TGEETYDIEGLGADFKPQQEVTLVIRGKDGSEKRVPVLLRIDTPIEVDYYKHGGILPFVL 899
Query: 896 RQLLAA 901
R LLAA
Sbjct: 900 RSLLAA 905
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: 2452
Number of extensions: 110
Number of successful extensions: 5
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: 905
Length adjustment: 43
Effective length of query: 858
Effective length of database: 862
Effective search space: 739596
Effective search space used: 739596
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 H281DRAFT_06606 H281DRAFT_06606 (aconitase)
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.12887.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 1314.4 0.0 0 1314.3 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06606 H281DRAFT_06606 aconitase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06606 H281DRAFT_06606 aconitase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1314.3 0.0 0 0 3 876 .] 19 903 .. 17 903 .. 0.97
Alignments for each domain:
== domain 1 score: 1314.3 bits; conditional E-value: 0
TIGR01341 3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkpa 67
++ysl++l ++ + ki++lp s+ri+lesvlrn dg+ki ee++ +l++wk ++ + ei+f ++
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 19 GKFYSLPQLGKAlNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHITQLANWKPTAPRVDEIPFVVS 84
579******998788*************************************************** PP
TIGR01341 68 rvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelef 133
rvvlqdftGvp++ d+aa+r +++gk+p+ i+plvpvdlv+dhsvq+d+++e++al+ n++lef
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 85 RVVLQDFTGVPLLADIAAMRGVAQRVGKNPKSIEPLVPVDLVVDHSVQIDHFREKNALDLNMKLEF 150
****************************************************************** PP
TIGR01341 134 ernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshtt 199
+rn+ery+f+kw+ +af +kvvppg Givhqvnleyla+ v+++ + +++ ypdslvGtdshtt
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 151 QRNNERYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTT 216
**********************************************99999*************** PP
TIGR01341 200 minGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvg 265
minG+Gv+GwGvGGieaea++lGqpv++ p+v+Gv+l+GklreGvtatdlvlt+tellrk+ vvg
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 217 MINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVNLKGKLREGVTATDLVLTITELLRKEKVVG 282
****************************************************************** PP
TIGR01341 266 kfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqe 331
kfveffGeg ++lsl+drati nmapeyGat++ffp+d++t++y++ tgr + +++ ++y kaq+
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 283 KFVEFFGEGTRSLSLPDRATIGNMAPEYGATMGFFPVDEKTIDYFKGTGRTDAEISAFQNYFKAQN 348
****************************************************************** PP
TIGR01341 332 lfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeak 396
lf + ++ +t+vv ldl +v +s+aGpkrpqdr+++ +vk++f ++++++e+g+a +
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 349 LFGIpKEGDIDFTKVVTLDLGTVAPSLAGPKRPQDRIEIGNVKSTFSDLFSKPVAENGFAKKEADL 414
**9877789**************************************************9987776 PP
TIGR01341 397 ekkle.gkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvv 461
+ + + ++k+g+v iaaitsctntsnpsvll+agllakkave+Gl v p++ktslapGs++v
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 415 DAQYTtSNGVNVKNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480
66544278899******************************************************* PP
TIGR01341 462 tdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihp 527
t+yl+++gllpyl++lGf+l yGcttciGn+G+l+ e++eai++nd++++avlsGnrnfe+rihp
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 481 TEYLTKTGLLPYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHP 546
****************************************************************** PP
TIGR01341 528 lvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfk 593
++an+laspplvvaya+aG+++ dl +ep+g +k Gk+vyl diwp+ +e+++l k a+ + f+
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 547 NIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDVYLGDIWPTSDEVNDLLKFALDADAFR 612
****************************************************************** PP
TIGR01341 594 keyeevtegnerwnelevtssdlyewdekstyireppff.eelklepee.vedikgarillllGds 657
k+y+++t++ + w ++e ++++y+w +kstyi eppff ++++++p++ + +k+ar l +Gds
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 613 KNYASLTKKGDLWSKIEGEEGQVYDW-PKSTYIAEPPFFgNDFSMTPADsIAAVKNARALGIFGDS 677
**************************.79**********55689999762678************* PP
TIGR01341 658 ittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgk... 720
+ttdhispaGsik+dspa+k+lke+Gv++ dfnsyGsrrGnh+vm+rGtfan+rikn ++++k
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 678 VTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGNHDVMMRGTFANVRIKNLMIPAKadg 743
***********************************************************9864333 PP
TIGR01341 721 ...eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaes 783
eGglt++ p +e++s+ydaamky + g+p++v aG+eyG+Gssrdwaakgt+llGvkav+a+s
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 744 srvEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTIVFAGEEYGTGSSRDWAAKGTQLLGVKAVVARS 809
3448************************************************************** PP
TIGR01341 784 ferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketve 848
ferihrsnlvgmGvlpl+fk ++ ++lg+tgeet d++++ + kp++evt+++ +dg+++ v
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 810 FERIHRSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLgADFKPQQEVTLVIRGKDGSEKRVP 875
****************************************7369********************** PP
TIGR01341 849 avlridtevelayvkkgGilqyvlrkll 876
+ lridt++e++y+k+gGil +vlr ll
lcl|FitnessBrowser__Burk376:H281DRAFT_06606 876 VLLRIDTPIEVDYYKHGGILPFVLRSLL 903
************************9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (905 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 10.37
//
[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