Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase
Query= reanno::Marino:GFF3491 (919 letters) >FitnessBrowser__Dyella79:N515DRAFT_1419 Length = 916 Score = 1130 bits (2923), Expect = 0.0 Identities = 568/913 (62%), Positives = 694/913 (76%), Gaps = 11/913 (1%) Query: 9 DSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSHID 68 DS T +L G ++ SL K D+ LP+S+K+L+ENLLR+EDG V I+ Sbjct: 3 DSFATRDTLKVNGSSYQIASLAKLGQRF-DIKHLPYSMKILLENLLRHEDGVNVTAKEIE 61 Query: 69 AMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSPVD 128 A+ +W DTEI F PARV++QDFTGVP VVDLAAMR+AV G D INPL+P + Sbjct: 62 AVARWNPKAEPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAE 121 Query: 129 LVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQVN 188 LVIDHSV VD +G S+ + NVAIE +RNQERY FLRWGQ+AFDNF+VVPP TGI HQVN Sbjct: 122 LVIDHSVQVDVYGSESALEQNVAIEFQRNQERYAFLRWGQKAFDNFKVVPPRTGIVHQVN 181 Query: 189 LEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPVSM 248 LEYLG+ V+ ++DG++ AYPDT+ GTDSHTTMING+G+LGWGVGGIEAEAAMLGQP SM Sbjct: 182 LEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGVGVLGWGVGGIEAEAAMLGQPSSM 241 Query: 249 LIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRATIA 308 LIP+VVGFK+TGKL EG+TATDLVLTVT+MLRK GVVGKFVEF+G GLKD+ +ADRATI Sbjct: 242 LIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLKDLALADRATIG 301 Query: 309 NMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWR-EPGHEPVYTDNL 367 NMAPEYGATCG FPVD++ + Y+RL+GR EE +ELV+AYA+AQGLW E +T L Sbjct: 302 NMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDENTPHAQFTTTL 361 Query: 368 ELDMGEVEASLAGPKRPQDRVALKNMKSSFELL---METAEGPAENREANLESEGGQTAV 424 ELD+G+V SLAGPKRPQDRV L++++ SF + P +N +EGG A+ Sbjct: 362 ELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRPRNGDTSNFINEGGSAAI 421 Query: 425 GVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGL 484 G + + +E NGE RL GAVVIAAITSCTNTSNP+VM+ AGL+A+KA KGL Sbjct: 422 GNPANAVSESGVLVEKNGESFRLGDGAVVIAAITSCTNTSNPAVMLGAGLLAKKAAAKGL 481 Query: 485 STKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAI 544 +PWVKTSL PGSKVVTDYL+ G +L+K+GF +VGYGCTTCIGNSGPLP + K I Sbjct: 482 KAQPWVKTSLGPGSKVVTDYLEKTGLLQELEKVGFYVVGYGCTTCIGNSGPLPAEISKGI 541 Query: 545 SDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDG 604 ++GDL VASVLSGNRNFEGRVHP VK N+LASPPLVVAYALAG++ +DLS+DPLG DG Sbjct: 542 AEGDLAVASVLSGNRNFEGRVHPEVKMNYLASPPLVVAYALAGSLDVDLSKDPLGTGSDG 601 Query: 605 NPVYLKDLWPSQQEIAEAVE-KVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKST 663 PVYL+D+WPS QEI++ + + MF K YA+VF GD W I P+ VY+W D ST Sbjct: 602 QPVYLRDIWPSNQEISDTIAGAINPAMFAKNYADVFQGDDRWNHIASPDGSVYQWGD-ST 660 Query: 664 YIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGV 723 YI++PP+F+G+ E ++DI A +L L GDS+TTDHISPAGS K D+PAG++L GV Sbjct: 661 YIKNPPYFDGMTREVGKVEDIHGARVLGLFGDSITTDHISPAGSIKKDSPAGRFLIGKGV 720 Query: 724 EPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQ 783 EPKDFNSYGSRRGN +VM+RGTFAN+RIRN MLDGVEGGYT VP+GEQ+AIYDAAMKY+ Sbjct: 721 EPKDFNSYGSRRGNDDVMVRGTFANIRIRNLMLDGVEGGYTLHVPSGEQLAIYDAAMKYK 780 Query: 784 EKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPE 843 + TPLVV+AGKEYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+P QF + Sbjct: 781 AEHTPLVVLAGKEYGTGSSRDWAAKGTLLLGVKAVIAESFERIHRSNLVGMGVLPCQFED 840 Query: 844 GTDRKSLKLTGEETISIEGLS-GEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902 G ++L LTG+E I GL+ GE K K+T DGS + +K + T E +F Sbjct: 841 GQSAQTLGLTGKEVFDITGLNDGESK---VAKVTATAPDGSRKEFIVKVLLLTPKEREFF 897 Query: 903 KHGGILHYVVREM 915 +HGGIL YV+R++ Sbjct: 898 RHGGILQYVLRQL 910 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: 2290 Number of extensions: 103 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: 919 Length of database: 916 Length adjustment: 43 Effective length of query: 876 Effective length of database: 873 Effective search space: 764748 Effective search space used: 764748 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 N515DRAFT_1419 N515DRAFT_1419 (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.12781.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 1375.9 0.0 0 1375.3 0.0 1.2 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 N515DRAFT_1419 aconitate hydrata Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1375.3 0.0 0 0 7 875 .. 22 910 .. 16 911 .. 0.96 Alignments for each domain: == domain 1 score: 1375.3 bits; conditional E-value: 0 TIGR01341 7 slkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72 sl +l + +i++lp+s++ille++lr+ dg +++ +++ea++ w+ ++ d+eiaf+parvvlq lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 22 SLAKLG-QRFDIKHLPYSMKILLENLLRHEDGVNVTAKEIEAVARWNPKAEPDTEIAFMPARVVLQ 86 555555.5678******************************************************* PP TIGR01341 73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernke 138 dftGvp vvdlaa+r+av +lg+d+++inpl p++lvidhsvqvd++g+e+ale+nv +ef+rn+e lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 87 DFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAELVIDHSVQVDVYGSESALEQNVAIEFQRNQE 152 ****************************************************************** PP TIGR01341 139 rykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGl 204 ry+fl+w++kaf n+kvvpp tGivhqvnleyl++vvf+ ekdg+ aypd++ GtdshttminG+ lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 153 RYAFLRWGQKAFDNFKVVPPRTGIVHQVNLEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGV 218 ****************************************************************** PP TIGR01341 205 GvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfvef 270 GvlGwGvGGieaeaa+lGqp+s+ +p+v+G+kltGkl eGvtatdlvltvt++lrk gvvgkfvef lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 219 GVLGWGVGGIEAEAAMLGQPSSMLIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEF 284 ****************************************************************** PP TIGR01341 271 fGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd. 335 fG+glk l+ladrati nmapeyGat+++fp+d+++l+ylrl+gr+e+++elv++y++aq+l++d lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 285 FGPGLKDLALADRATIGNMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDe 350 *****************************************************************5 PP TIGR01341 336 dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalr......... 392 ++ ++++t+++eldl dv++s+aGpkrpqdrv l++v+++f+ +l ++++ lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 351 NTPHAQFTTTLELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRPRNGdtsnfineg 416 55669**************************************97654444432111223455678 PP TIGR01341 393 .............keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlk 445 + +g++ +l dgavviaaitsctntsnp+v+lgagllakka Glk lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 417 gsaaignpanavsESGVLVEKNGESFRLGDGAVVIAAITSCTNTSNPAVMLGAGLLAKKAAAKGLK 482 88888877764332222233359999**************************************** PP TIGR01341 446 vkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlev 511 +p+vktsl pGskvvtdyl ++gll+ le++Gf++vGyGcttciGnsGpl+ e+++ i+e+dl v lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 483 AQPWVKTSLGPGSKVVTDYLEKTGLLQELEKVGFYVVGYGCTTCIGNSGPLPAEISKGIAEGDLAV 548 ****************************************************************** PP TIGR01341 512 savlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsak 577 ++vlsGnrnfegr+hp vk nylaspplvvayalaG++d+dl+k+p+gt+ dG++vyl+diwps++ lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 549 ASVLSGNRNFEGRVHPEVKMNYLASPPLVVAYALAGSLDVDLSKDPLGTGSDGQPVYLRDIWPSNQ 614 ****************************************************************** PP TIGR01341 578 eiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeeve 643 ei++++ a+++ +f k+y+ v++g++rwn++ +++++y+w +styi++pp+f++++ e +ve lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 615 EISDTIAGAINPAMFAKNYADVFQGDDRWNHIASPDGSVYQWG-DSTYIKNPPYFDGMTREVGKVE 679 ******************************************6.7********************* PP TIGR01341 644 dikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfan 709 di+gar+l l+GdsittdhispaGsikkdspa+++l+ kGve++dfnsyGsrrGn++vm+rGtfan lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 680 DIHGARVLGLFGDSITTDHISPAGSIKKDSPAGRFLIGKGVEPKDFNSYGSRRGNDDVMVRGTFAN 745 ****************************************************************** PP TIGR01341 710 iriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllG 775 iri+n +++g eGg+t+++p +e++++ydaamkyk e++plvvlaGkeyG+Gssrdwaakgt llG lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 746 IRIRNLMLDGVEGGYTLHVPSGEQLAIYDAAMKYKAEHTPLVVLAGKEYGTGSSRDWAAKGTLLLG 811 ****************************************************************** PP TIGR01341 776 vkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvked 841 vkaviaesferihrsnlvgmGvlp +f++g++a+tlgltg+e d+ ++++ + k ++v+++ d lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 812 VKAVIAESFERIHRSNLVGMGVLPCQFEDGQSAQTLGLTGKEVFDITGLNDGES-KVAKVTATAPD 876 ***********************************************9999765.5689******* PP TIGR01341 842 geketveavlridtevelayvkkgGilqyvlrkl 875 g+++ + +++ + t+ e +++++gGilqyvlr+l lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 877 GSRKEFIVKVLLLTPKEREFFRHGGILQYVLRQL 910 *******************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (916 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09 # Mc/sec: 8.81 // [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