Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_086509646.1 BZY95_RS09205 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683 (865 letters) >NCBI__GCF_002151265.1:WP_086509646.1 Length = 867 Score = 1370 bits (3547), Expect = 0.0 Identities = 671/861 (77%), Positives = 752/861 (87%), Gaps = 1/861 (0%) Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60 MLE YR+HV ERAAEG+ PKPL+A Q AALVELLKNPPAGEEEF+LDLLTNR+PPGVDEA Sbjct: 1 MLEAYRQHVEERAAEGVPPKPLNAEQAAALVELLKNPPAGEEEFVLDLLTNRIPPGVDEA 60 Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 AYVKAGFL AI KGEA+SPL+ A++LLGTMQGGYNI L++ LDDA+LA A + L Sbjct: 61 AYVKAGFLTAITKGEAQSPLVDKVHAVKLLGTMQGGYNIATLVELLDDAELAKEAGEQLK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180 HTLLMFD F+DVEE+AKAGN AK VMQSWA+AEWFL++PALAEK+T+TVFKV GETNTD Sbjct: 121 HTLLMFDAFHDVEERAKAGNAVAKDVMQSWAEAEWFLSKPALAEKITLTVFKVPGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240 DLSPAPDAWSRPDIPLHA AMLKN REGI P+ PG GP+KQIE ++ KG+P+AYVGDVV Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKNEREGIVPEVPGTTGPLKQIEEVKAKGYPVAYVGDVV 240 Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300 GTGSSRKSATNSVLWF GDDIP+VPNKR GG C GGKIAPIFFNTMEDAGALP+E+DVS Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGGKIAPIFFNTMEDAGALPVEMDVSK 300 Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360 L MGDVIDVYPY+G+V H T E+L TFELKT V++DEVRAGGRIPLIIGRGLT KARE+ Sbjct: 301 LEMGDVIDVYPYEGKVCKHGTDEVLTTFELKTQVILDEVRAGGRIPLIIGRGLTGKARES 360 Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420 LGL SDVFR + ++ +GF+LAQKMVG+ACG+ G+RPG YCEPKMT+VGSQDTTGPM Sbjct: 361 LGLAPSDVFRLPEQPKDTGKGFTLAQKMVGKACGMAGVRPGMYCEPKMTTVGSQDTTGPM 420 Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480 TRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDG+IH Sbjct: 421 TRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIH 480 Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540 SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKR 540 Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600 QPG+TLRDLVHAIP YAIKQGLLTV K GKKN FSGR+LEIEGL DL VEQAFEL+DASA Sbjct: 541 QPGVTLRDLVHAIPYYAIKQGLLTVAKAGKKNAFSGRVLEIEGLEDLTVEQAFELSDASA 600 Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660 ERSAAGCTI L + + EYL SNI LLKWMIA GYGD+RT+ERRI ME+WLANP L+ A Sbjct: 601 ERSAAGCTITLGEASVTEYLKSNITLLKWMIANGYGDKRTIERRILAMEEWLANPSLMRA 660 Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720 D DAEYA VI+IDL ++KEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHFRAA Sbjct: 661 DKDAEYAEVIEIDLDELKEPVLCAPNDPDDARLLSEVAGEKIDEVFIGSCMTNIGHFRAA 720 Query: 721 GKLLDAH-KGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779 GKLL+ G L TRLW+APPT+MD QLTEEGYY ++G++GAR+E+PGCSLCMGNQARV Sbjct: 721 GKLLEKQPAGSLKTRLWLAPPTKMDQHQLTEEGYYGIYGRAGARMEMPGCSLCMGNQARV 780 Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVD 839 A +TVVSTSTRNFPNRLG GANV+LASAELAAVAA+ G+LP+ EEYQ Y+ + D A + Sbjct: 781 AAKSTVVSTSTRNFPNRLGDGANVYLASAELAAVAAVEGRLPSVEEYQRYMGEFDAMAGE 840 Query: 840 TYRYLNFNQLSQYTEKADGVI 860 YRY+NF+++ +Y A VI Sbjct: 841 IYRYMNFHEIEEYQNAASNVI 861 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: 2191 Number of extensions: 73 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: 867 Length adjustment: 42 Effective length of query: 823 Effective length of database: 825 Effective search space: 678975 Effective search space used: 678975 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)
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