Align aconitase (EC 4.2.1.3) (characterized)
to candidate WP_013460045.1 SULKU_RS05970 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= metacyc::HP0779-MONOMER (852 letters) >NCBI__GCF_000183725.1:WP_013460045.1 Length = 869 Score = 1084 bits (2804), Expect = 0.0 Identities = 544/859 (63%), Positives = 660/859 (76%), Gaps = 19/859 (2%) Query: 4 FLEDYKKSVSERGSEGIPPLPLNAKQVQAVVEILTKDPTNAAFAKELLIHRVSPGVDEGA 63 F+++YK V+ER ++GIPPLPL +QV A+VE++T + + A E+L RV+PGVD+GA Sbjct: 3 FMDEYKAHVAEREAQGIPPLPLTKEQVTALVELITAESSKNAELVEMLAERVNPGVDDGA 62 Query: 64 KVKAEFLAKLSQKKLECVHISALE---------ATTLLGTMLGGYNVEPLIMGLESQDKN 114 VKA FL ++ Q +++ + A +LG M+GGYNV+PLI L + Sbjct: 63 HVKAAFLHQVVQGQVKAFLADNSDINSDDHKKAAIKILGKMVGGYNVKPLIDALSNDA-- 120 Query: 115 IAKESAKALKTTLLVYGSFDKIAAMSKTNALAKEVLESWANAEWFLNKEPLNECIEACVF 174 IA E+A LK TLLVY +F+ I +S+TN AKEVL+SWA+AEWF K+PL E VF Sbjct: 121 IANEAAHELKHTLLVYDAFNDIVDLSQTNKYAKEVLQSWADAEWFTAKKPLAEKFSVVVF 180 Query: 175 KIDGETNTDDLSPASDAFTRSDIPLHAKAMLKNRIENYEQRIKAIKTKGVPVAYVGDVVG 234 K GETNTDDLSPAS AFTRSDIPLHA ML ++ +I +K G +AYVGDVVG Sbjct: 181 KFPGETNTDDLSPASAAFTRSDIPLHATTMLSAKMPEGIAKIAELKKMGKQIAYVGDVVG 240 Query: 235 TGSSRKSATNSIMWHFGKDIPFVPNKRSGGIVIGGVIAPIFFATCEDSGALPIVADVKDL 294 TGSSRKSA NS+ WH G DIP +PNKR+GG+VIG +IAPIFFATCEDSGALPI ADV + Sbjct: 241 TGSSRKSAANSVQWHMGDDIPGIPNKRTGGVVIGSIIAPIFFATCEDSGALPIEADVSQM 300 Query: 295 KEGDLIKIYPYKGEITLNDKVVSTFKLEPETLLDEVRASGRIPLIIGRGLTNKARKFLGL 354 + GD++ I G IT N ++TF L P T+ DEVRA GRIPLIIGRGLT KAR LG+ Sbjct: 301 ETGDVLDIDTKAGTITKNGTQIATFSLRPNTIEDEVRAGGRIPLIIGRGLTAKARAALGM 360 Query: 355 GESEAFKKPSAPKSDAKGYTLAQKIVGHACGVKGILPGTYCEPKVTTVGSQDTTGAMTRD 414 + F P P KGYTLAQK+VG ACG++G+ PG YCEP +TVGSQDTTG MTRD Sbjct: 361 APATIFATPIQPADTGKGYTLAQKMVGKACGMEGVRPGMYCEPMTSTVGSQDTTGPMTRD 420 Query: 415 EVKELASLKFDAPFVLQSFCHTAAYPKPSDVSLHATLPGFITQRGGVALHPGDGVIHTWL 474 E+KEL++L F A FVLQSFCHTAAYPKPSDV LHATLP FI+ R GVAL P DGVIH+WL Sbjct: 421 EIKELSALGFSADFVLQSFCHTAAYPKPSDVKLHATLPAFISSRSGVALRPADGVIHSWL 480 Query: 475 NRMGLPDTLGTGGDSHTRFPLGISFPAGSGLVAFAAVTGTMPLNMPESVLVRFKGEMNPG 534 NRM LPDT+GTGGDSHTRFP+G+SFPAGSGLVAFAAVTG+MPL MPESVLVRFKGEM PG Sbjct: 481 NRMVLPDTVGTGGDSHTRFPIGVSFPAGSGLVAFAAVTGSMPLEMPESVLVRFKGEMQPG 540 Query: 535 ITLRDLVNAIPYYAIKKGLLTVEKKGKINVFNGRILEIEGLPDIKMEQAFELSDASAERS 594 ITLRDLVNAIPYYAIK+GLLTVEKKGK N+FNGR+LEIEGLP++K+EQAFELSDASAERS Sbjct: 541 ITLRDLVNAIPYYAIKQGLLTVEKKGKKNIFNGRVLEIEGLPNMKVEQAFELSDASAERS 600 Query: 595 AAACVVRLNKEPMIEYLKSNIKLIDEMIASGYEDKETLKKRRDAMQAWVDNPVLLEPDSN 654 AAAC VRLNKEP+IEYLKSN+ LI+ MI GYED TL++R D M+ W+ P L+EPD++ Sbjct: 601 AAACTVRLNKEPVIEYLKSNVTLIEAMIKDGYEDARTLQRRADKMKEWLAAPSLMEPDAD 660 Query: 655 AQYAAVIEIDVAEITEPILACPNDPDDVATLSEVLADTTGKRPHAIDEVFIGSCMTNIGH 714 A+YAA+IEID+ E+ EPILACPNDPD+V LSEV + IDEVF+GSCMTNIGH Sbjct: 661 AEYAAIIEIDLNEVKEPILACPNDPDNVKLLSEVAGE-------KIDEVFLGSCMTNIGH 713 Query: 715 FRAFGEIVK-NAPPSQARLWVVPPSKMDEQELINEGYYAIFGAAGARTEVPGCSLCMGNQ 773 +RA GE+++ + + W+VPP++MDEQ+LINEGYY ++ A A+TEVPGCSLCMGNQ Sbjct: 714 YRAAGEVMRGEGKIAVEKFWIVPPTRMDEQQLINEGYYDVYKAIAAQTEVPGCSLCMGNQ 773 Query: 774 ARVRDNAVVFSTSTRNFDNRMGRGAKVYLGSAELGAACALLGRIPTKEEYMNLVSEKLES 833 A R+ + VFSTSTRNFDNR+G+G +VYLGSAEL A CA LGRIPT EYM++V EKL Sbjct: 774 ASSREGSTVFSTSTRNFDNRLGKGTQVYLGSAELAAVCAKLGRIPTVAEYMSIVPEKLAG 833 Query: 834 QKDKIYRYMNFNLMENFRL 852 + D +Y+Y+NFN + ++ L Sbjct: 834 KADDVYKYLNFNEIASYSL 852 Lambda K H 0.317 0.135 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: 1828 Number of extensions: 71 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: 852 Length of database: 869 Length adjustment: 42 Effective length of query: 810 Effective length of database: 827 Effective search space: 669870 Effective search space used: 669870 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 (21.6 bits) S2: 56 (26.2 bits)
Align candidate WP_013460045.1 SULKU_RS05970 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (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/TIGR00117.hmm # target sequence database: /tmp/gapView.1365623.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00117 [M=844] Accession: TIGR00117 Description: acnB: aconitate hydratase 2 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 1443.7 1.8 0 1443.5 1.8 1.0 1 NCBI__GCF_000183725.1:WP_013460045.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000183725.1:WP_013460045.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1443.5 1.8 0 0 1 843 [. 3 851 .. 3 852 .. 0.98 Alignments for each domain: == domain 1 score: 1443.5 bits; conditional E-value: 0 TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73 +++ey+ hvaer+a+gi+plpl +qv+alvel++ + ++ +++l+e+l +rv+pgvd++a+vka fl ++ + NCBI__GCF_000183725.1:WP_013460045.1 3 FMDEYKAHVAEREAQGIPPLPLTKEQVTALVELITAESSK-NAELVEMLAERVNPGVDDGAHVKAAFLHQVVQ 74 579********************************99887.88899*************************** PP TIGR00117 74 gevkspl.....isa....eeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveel 137 g+vk+ l i + + a+++lg m+ggynv+pli+al + ia++aa+ l++tllv+daf+d+ +l NCBI__GCF_000183725.1:WP_013460045.1 75 GQVKAFLadnsdINSddhkKAAIKILGKMVGGYNVKPLIDALS--NDAIANEAAHELKHTLLVYDAFNDIVDL 145 ***9876222223322222569********************9..678************************* PP TIGR00117 138 sktneyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieei 210 s+tn+yak+vl+swa+aewf k++laek++v+vfk +getntddlspa+ aftr+diplha +ml +k++e NCBI__GCF_000183725.1:WP_013460045.1 146 SQTNKYAKEVLQSWADAEWFTAKKPLAEKFSVVVFKFPGETNTDDLSPASAAFTRSDIPLHATTMLSAKMPEG 218 ************************************************************************* PP TIGR00117 211 eqrikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgal 283 +i++lk+ g +ayvgdvvgtgssrksa nsv w++g+dip +pnkr+gg+v+g iapiff+t+edsgal NCBI__GCF_000183725.1:WP_013460045.1 219 IAKIAELKKMGKQIAYVGDVVGTGSSRKSAANSVQWHMGDDIPGIPNKRTGGVVIGSIIAPIFFATCEDSGAL 291 ************************************************************************* PP TIGR00117 284 pievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglses 356 pie+dv+++++gdv++i + g it++ +atf l+p+t+ devraggripliigrglt kar alg++++ NCBI__GCF_000183725.1:WP_013460045.1 292 PIEADVSQMETGDVLDIDTKAGTITKNG-TQIATFSLRPNTIEDEVRAGGRIPLIIGRGLTAKARAALGMAPA 363 *************************987.679***************************************** PP TIGR00117 357 evfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvl 429 +f + +pa+++kg+tlaqk+vgkacg++g+rpg ycep+ +tvgsqdttg+mtrde+kel++lgf+ad+vl NCBI__GCF_000183725.1:WP_013460045.1 364 TIFATPIQPADTGKGYTLAQKMVGKACGMEGVRPGMYCEPMTSTVGSQDTTGPMTRDEIKELSALGFSADFVL 436 ************************************************************************* PP TIGR00117 430 qsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpags 502 qsfchtaaypkp+dvk+h+tlp fis+r gvalrp dgvihswlnrm+lpdtvgtggdshtrfp+g+sfpags NCBI__GCF_000183725.1:WP_013460045.1 437 QSFCHTAAYPKPSDVKLHATLPAFISSRSGVALRPADGVIHSWLNRMVLPDTVGTGGDSHTRFPIGVSFPAGS 509 ************************************************************************* PP TIGR00117 503 glvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglp 575 glvafaa+tg mpl+mpesvlvrfkge+qpgitlrdlvnaipyyaik+glltvekkgk+n+fngr+leieglp NCBI__GCF_000183725.1:WP_013460045.1 510 GLVAFAAVTGSMPLEMPESVLVRFKGEMQPGITLRDLVNAIPYYAIKQGLLTVEKKGKKNIFNGRVLEIEGLP 582 ************************************************************************* PP TIGR00117 576 dlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpell 648 ++kveqafel+dasaersaa+ct++lnkepvieylksn+ l++ mi +gyed+rtl+rr d+m++wla p+l+ NCBI__GCF_000183725.1:WP_013460045.1 583 NMKVEQAFELSDASAERSAAACTVRLNKEPVIEYLKSNVTLIEAMIKDGYEDARTLQRRADKMKEWLAAPSLM 655 ************************************************************************* PP TIGR00117 649 eadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaaktv. 720 e+dadaeyaa+ieidl+e+kepila+pndpd+vkllsevag++idevf+gscmtnigh+raag+++ +++++ NCBI__GCF_000183725.1:WP_013460045.1 656 EPDADAEYAAIIEIDLNEVKEPILACPNDPDNVKLLSEVAGEKIDEVFLGSCMTNIGHYRAAGEVMRGEGKIa 728 ********************************************************************99651 PP TIGR00117 721 karlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvy 793 ++w+vpptrmdeqqli+egyy ++ a a+tevpgcslcmgnqa ++g+tvfststrnfdnrlgkg++vy NCBI__GCF_000183725.1:WP_013460045.1 729 VEKFWIVPPTRMDEQQLINEGYYDVYKAIAAQTEVPGCSLCMGNQASSREGSTVFSTSTRNFDNRLGKGTQVY 801 579********************************************************************** PP TIGR00117 794 lgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843 lgsaelaav+a lg+ipt+ ey+++v ek++ + d++y+ylnfne+ + NCBI__GCF_000183725.1:WP_013460045.1 802 LGSAELAAVCAKLGRIPTVAEYMSIVPEKLAGKADDVYKYLNFNEIASYS 851 **********************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (844 nodes) Target sequences: 1 (869 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 19.33 // [ok]
This GapMind analysis is from Apr 09 2024. 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