Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1
Query= reanno::Marino:GFF3491 (919 letters) >FitnessBrowser__Marino:GFF3491 Length = 919 Score = 1845 bits (4780), Expect = 0.0 Identities = 919/919 (100%), Positives = 919/919 (100%) Query: 1 MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT 60 MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT Sbjct: 1 MSNESLSKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGT 60 Query: 61 TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM 120 TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM Sbjct: 61 TVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAM 120 Query: 121 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG 180 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG Sbjct: 121 INPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPG 180 Query: 181 TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA 240 TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA Sbjct: 181 TGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAA 240 Query: 241 MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP 300 MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP Sbjct: 241 MLGQPVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMP 300 Query: 301 VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE 360 VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE Sbjct: 301 VADRATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE 360 Query: 361 PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG 420 PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG Sbjct: 361 PVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGG 420 Query: 421 QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480 QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV Sbjct: 421 QTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480 Query: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV Sbjct: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540 Query: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN Sbjct: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600 Query: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD Sbjct: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660 Query: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE Sbjct: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720 Query: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM Sbjct: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780 Query: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ Sbjct: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840 Query: 841 FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900 FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV Sbjct: 841 FPEGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900 Query: 901 YFKHGGILHYVVREMLRTA 919 YFKHGGILHYVVREMLRTA Sbjct: 901 YFKHGGILHYVVREMLRTA 919 Lambda K H 0.315 0.134 0.390 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: 2757 Number of extensions: 100 Number of successful extensions: 1 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: 919 Length of database: 919 Length adjustment: 43 Effective length of query: 876 Effective length of database: 876 Effective search space: 767376 Effective search space used: 767376 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: 42 (22.0 bits) S2: 57 (26.6 bits)
Align candidate GFF3491 HP15_3433 (aconitate hydratase 1)
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.2110072.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 1461.1 0.0 0 1460.9 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3491 HP15_3433 aconitate hydratase 1 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3491 HP15_3433 aconitate hydratase 1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1460.9 0.0 0 0 1 876 [] 22 916 .. 22 916 .. 0.97 Alignments for each domain: == domain 1 score: 1460.9 bits; conditional E-value: 0 TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75 k+ +yysl++++++l+++++lp sl++l+e++lrn dg+++ ++++a+++w k+ ++d+ei+f+parv++qdft lcl|FitnessBrowser__Marino:GFF3491 22 KTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSHIDAMVQWMKDRHSDTEIQFRPARVLMQDFT 96 689************************************************************************ PP TIGR01341 76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150 Gvp vvdlaa+reav++ gkdp++inpl+pvdlvidhsv vdk+g+ ++++ nv +e+ern+ery+fl+w+++af lcl|FitnessBrowser__Marino:GFF3491 97 GVPGVVDLAAMREAVQAAGKDPAMINPLSPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAF 171 *************************************************************************** PP TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225 n++vvppgtGi+hqvnleyl+k v+++++dg+++aypd+lvGtdshttminGlG+lGwGvGGieaeaa+lGqpv lcl|FitnessBrowser__Marino:GFF3491 172 DNFRVVPPGTGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246 *************************************************************************** PP TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300 s+ +pev+G+k+tGklreG+tatdlvltvte+lrkkgvvgkfvef+G+glk +++adratianmapeyGat++ff lcl|FitnessBrowser__Marino:GFF3491 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRATIANMAPEYGATCGFF 321 *************************************************************************** PP TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaa 375 p+d++t++y+rltgr+e+++elve+y+kaq+l+++ ++ep+ytd +eld+ +veas+aGpkrpqdrvalk++k++ lcl|FitnessBrowser__Marino:GFF3491 322 PVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKSS 396 *************************************************************************** PP TIGR01341 376 fkssles...nagekglalr................keakekklegkeaelkdgavviaaitsctntsnpsvllg 431 f+ +e+ +a +++ +l+ + ++ ++g++ +l+ gavviaaitsctntsnpsv+++ lcl|FitnessBrowser__Marino:GFF3491 397 FELLMETaegPAENREANLEseggqtavgvddsykhHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMA 471 *86544311144556656656666666666688865556667889****************************** PP TIGR01341 432 agllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaike 506 agl+a+kav+ Gl kp+vktslapGskvvtdyl+ g+++ l++lGfnlvGyGcttciGnsGpl+++ve+ai + lcl|FitnessBrowser__Marino:GFF3491 472 AGLIAQKAVQKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAISD 546 *************************************************************************** PP TIGR01341 507 ndlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581 +dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +dl+++p+g dkdG++vylkd+wps++eiae lcl|FitnessBrowser__Marino:GFF3491 547 GDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGNPVYLKDLWPSQQEIAE 621 *************************************************************************** PP TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGd 656 +v ++vk+++f+key+ev++g+++w++++v++s++yew +kstyi++ppffe+lk ep+ ++dik+a il+llGd lcl|FitnessBrowser__Marino:GFF3491 622 AV-EKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGD 695 65.68********************************************************************** PP TIGR01341 657 sittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpds 731 s+ttdhispaGs k+d+pa+kyl+e+Gve++dfnsyGsrrGnhevm+rGtfan+ri+n++++g eGg+t+++p++ lcl|FitnessBrowser__Marino:GFF3491 696 SVTTDHISPAGSFKPDTPAGKYLQEHGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTG 770 *************************************************************************** PP TIGR01341 732 evvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqge 806 e++++ydaamky+++g+plvv+aGkeyG+Gssrdwaakgt+llGvkav+aes+erihrsnl+gmGv+pl+f++g+ lcl|FitnessBrowser__Marino:GFF3491 771 EQMAIYDAAMKYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845 *************************************************************************** PP TIGR01341 807 daetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876 d+++l ltgeeti ++++ e+kp++++++++ +dg+ et e + ridt+ e y+k+gGil+yv+r++l lcl|FitnessBrowser__Marino:GFF3491 846 DRKSLKLTGEETISIEGLsGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKHGGILHYVVREML 916 *****************6269***********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (919 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 30.59 // [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