Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_029132406.1 A3GO_RS0104620 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >NCBI__GCF_000428045.1:WP_029132406.1 Length = 862 Score = 1388 bits (3592), Expect = 0.0 Identities = 681/861 (79%), Positives = 757/861 (87%), Gaps = 1/861 (0%) Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60 MLE YRKHV ERAA+GI P PL+ Q A LVELLK PP GEE +LLDL+I+RVP GVD++ Sbjct: 1 MLESYRKHVEERAAEGIPPLPLNPEQTAQLVELLKNPPAGEEAYLLDLIIHRVPAGVDQS 60 Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKA FLA VAKG PL+ KA ELLGTM GGYNI PL++ALDD LAP A KALS Sbjct: 61 AYVKAAFLADVAKGSCNCPLIDRVKATELLGTMLGGYNIAPLVEALDDEALAPTAVKALS 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180 HTLL+FD F DV+EKA AGN++AK ++QSWA+ EWF +P LAEK+T+TVFKVTGETNTD Sbjct: 121 HTLLVFDAFNDVKEKADAGNDHAKAILQSWAEGEWFTQKPELAEKVTLTVFKVTGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240 DLSPAPDAWSRPDIPLHA AMLK REGI PDQPGV+GPIK IE L++KG+P+AYVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKMEREGITPDQPGVIGPIKFIEELKQKGHPVAYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLW MGDDIP +PNKR GG CLGGKIAPIFFNTMEDAGALP E DVSN Sbjct: 241 GTGSSRKSATNSVLWHMGDDIPFIPNKRAGGFCLGGKIAPIFFNTMEDAGALPFECDVSN 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 LNMGDVIDVYPY+G V+NHE+GE L FELKTDVL+DEVRAGGRIPLIIGRGLT +AREA Sbjct: 301 LNMGDVIDVYPYEGVVKNHESGEELCRFELKTDVLLDEVRAGGRIPLIIGRGLTARAREA 360 Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420 LGL S +F+ A+S++G+SLAQKMVGRACGV+G+RPGAYCEP+MT+VGSQDTTGPM Sbjct: 361 LGLDPSTLFKSPAPAADSTKGYSLAQKMVGRACGVEGVRPGAYCEPRMTTVGSQDTTGPM 420 Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVD+TTHHTLPDFI +RGGV+LRPGDG+IH Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDITTHHTLPDFISSRGGVALRPGDGIIH 480 Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540 SWLNRMLLPDT+GTGGDSHTRFPIG+SFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM Sbjct: 481 SWLNRMLLPDTLGTGGDSHTRFPIGLSFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540 Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600 QPGITLRDLV+AIP YAIKQGLLTV K GKKNIFSGR+LEIEGLPDLKVEQAFEL+DASA Sbjct: 541 QPGITLRDLVNAIPYYAIKQGLLTVAKAGKKNIFSGRVLEIEGLPDLKVEQAFELSDASA 600 Query: 601 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660 ERSAAGCTIKL+K PI+EYL SNI LLKWMIA Y D RTL+RRI+GMEKWLADPQLLE Sbjct: 601 ERSAAGCTIKLDKAPIIEYLQSNITLLKWMIANDYQDPRTLQRRIEGMEKWLADPQLLEG 660 Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 720 DADAEYAAVI+IDLAD+KEPIL PNDPDD + LS+V G+KIDEVFIGSCMTNIGHFRAA Sbjct: 661 DADAEYAAVIEIDLADVKEPILACPNDPDDVKQLSEVAGQKIDEVFIGSCMTNIGHFRAA 720 Query: 721 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780 GKLL+ K +PTRLW+APPT+MDA L EEGYY+ FGK+GAR+E+PGCSLCMGNQARV Sbjct: 721 GKLLEG-KHDIPTRLWMAPPTKMDAYVLNEEGYYATFGKAGARMEMPGCSLCMGNQARVK 779 Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840 D ATVVSTSTRNFPNRLGTGANV+L+SAELAAVAA+IGKLPT EEY Y Q+D + D Sbjct: 780 DNATVVSTSTRNFPNRLGTGANVYLSSAELAAVAAIIGKLPTVEEYMVYADQIDAMSADI 839 Query: 841 YRYLNFDQLSQYTEKADGVIF 861 +RY+NFDQ+ Y A+ V F Sbjct: 840 FRYMNFDQIEAYQSVANRVEF 860 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: 2125 Number of extensions: 72 Number of successful extensions: 2 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: 865 Length of database: 862 Length adjustment: 42 Effective length of query: 823 Effective length of database: 820 Effective search space: 674860 Effective search space used: 674860 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 WP_029132406.1 A3GO_RS0104620 (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.3313384.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 1575.8 0.0 0 1575.6 0.0 1.0 1 NCBI__GCF_000428045.1:WP_029132406.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000428045.1:WP_029132406.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1575.6 0.0 0 0 1 843 [. 1 852 [. 1 853 [. 0.99 Alignments for each domain: == domain 1 score: 1575.6 bits; conditional E-value: 0 TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73 +le yrkhv eraaegi+plpln +q+a+lvellkn+p++ee++ll+l+i+rvp gvd++ayvka fla +ak NCBI__GCF_000428045.1:WP_029132406.1 1 MLESYRKHVEERAAEGIPPLPLNPEQTAQLVELLKNPPAGEEAYLLDLIIHRVPAGVDQSAYVKAAFLADVAK 73 79*********************************************************************** PP TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145 g ++pli +a+ellgtmlggyn+ pl+eal+ d+ +a++a kals+tllvfdaf+dv+e++++ n++ak NCBI__GCF_000428045.1:WP_029132406.1 74 GSCNCPLIDRVKATELLGTMLGGYNIAPLVEALD--DEALAPTAVKALSHTLLVFDAFNDVKEKADAgNDHAK 144 **********************************..*******************************9***** PP TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...... 212 +l+swae+ewf +k+elaek+t tvfkv+getntddlspapda++rpdiplha amlk ++e+i + NCBI__GCF_000428045.1:WP_029132406.1 145 AILQSWAEGEWFTQKPELAEKVTLTVFKVTGETNTDDLSPAPDAWSRPDIPLHANAMLKMEREGITPdqpgvi 217 *****************************************************************9999**** PP TIGR00117 213 ....rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsg 281 i++lkqkg+pvayvgdvvgtgssrksatnsvlw++g+dipf+pnkragg++lggkiapiffnt+ed+g NCBI__GCF_000428045.1:WP_029132406.1 218 gpikFIEELKQKGHPVAYVGDVVGTGSSRKSATNSVLWHMGDDIPFIPNKRAGGFCLGGKIAPIFFNTMEDAG 290 ***99******************************************************************** PP TIGR00117 282 alpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealgl 353 alp e+dv++ln+gdvi++ypy+g ++n+e+ e ++ f+lk+++lldevraggripliigrglt +arealgl NCBI__GCF_000428045.1:WP_029132406.1 291 ALPFECDVSNLNMGDVIDVYPYEGVVKNHESgEELCRFELKTDVLLDEVRAGGRIPLIIGRGLTARAREALGL 363 *****************************988***************************************** PP TIGR00117 354 sesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426 +s +fk ++ +a+s+kg++laqk+vg+acgv+g+rpg+ycep++ttvgsqdttg+mtrdelk+la+lgf+ad NCBI__GCF_000428045.1:WP_029132406.1 364 DPSTLFKSPAPAADSTKGYSLAQKMVGRACGVEGVRPGAYCEPRMTTVGSQDTTGPMTRDELKDLACLGFSAD 436 ************************************************************************* PP TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfp 499 lv+qsfchtaaypkpvd+ th+tlpdfis+rggvalrpgdg+ihswlnrmllpdt+gtggdshtrfp+g+sfp NCBI__GCF_000428045.1:WP_029132406.1 437 LVMQSFCHTAAYPKPVDITTHHTLPDFISSRGGVALRPGDGIIHSWLNRMLLPDTLGTGGDSHTRFPIGLSFP 509 ************************************************************************* PP TIGR00117 500 agsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileie 572 agsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlvnaipyyaik+glltv k gk+n+f+gr+leie NCBI__GCF_000428045.1:WP_029132406.1 510 AGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVNAIPYYAIKQGLLTVAKAGKKNIFSGRVLEIE 582 ************************************************************************* PP TIGR00117 573 glpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanp 645 glpdlkveqafel+dasaersaagctikl+k p+ieyl+sni llk+mia+ y+d rtl+rri++mekwla+p NCBI__GCF_000428045.1:WP_029132406.1 583 GLPDLKVEQAFELSDASAERSAAGCTIKLDKAPIIEYLQSNITLLKWMIANDYQDPRTLQRRIEGMEKWLADP 655 ************************************************************************* PP TIGR00117 646 elleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak 718 +lle+dadaeyaavieidla++kepila+pndpddvk+lsevag++idevfigscmtnighfraagk+le+++ NCBI__GCF_000428045.1:WP_029132406.1 656 QLLEGDADAEYAAVIEIDLADVKEPILACPNDPDDVKQLSEVAGQKIDEVFIGSCMTNIGHFRAAGKLLEGKH 728 ************************************************************************* PP TIGR00117 719 tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgak 791 ++++rlw++ppt+md+ l eegyya fg+agar+e+pgcslcmgnqarv+d+atv+ststrnf+nrlg+ga+ NCBI__GCF_000428045.1:WP_029132406.1 729 DIPTRLWMAPPTKMDAYVLNEEGYYATFGKAGARMEMPGCSLCMGNQARVKDNATVVSTSTRNFPNRLGTGAN 801 ************************************************************************* PP TIGR00117 792 vylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843 vyl+saelaavaa++gk+pt+eey+ + + ++ d ++ry+nf+++e ++ NCBI__GCF_000428045.1:WP_029132406.1 802 VYLSSAELAAVAAIIGKLPTVEEYMVYADQIDAMSAD-IFRYMNFDQIEAYQ 852 *************************998888877777.***********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (844 nodes) Target sequences: 1 (862 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 42.86 // [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