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_028313028.1 H566_RS0121290 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >NCBI__GCF_000482785.1:WP_028313028.1 Length = 863 Score = 1273 bits (3294), Expect = 0.0 Identities = 647/864 (74%), Positives = 728/864 (84%), Gaps = 8/864 (0%) Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60 MLE YR+HVAERAA GI P PL A Q A L+EL+K PP GEE+FL++LL RVPPGVD+A Sbjct: 1 MLETYRQHVAERAALGIPPLPLSAQQTADLIELIKNPPAGEEDFLVELLTFRVPPGVDDA 60 Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120 A VKA FLAAVA GD L+S KA ELLGTM GGYN+ PLID L+D ++A IAA+ L Sbjct: 61 AKVKASFLAAVAHGDIKVGLISKAKATELLGTMVGGYNVKPLIDLLEDGEVAAIAAEGLK 120 Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180 TLLMFD F+DV EKAKAGN AK+V+QSWADAEWF +RP + + ITVTVFKV GETNTD Sbjct: 121 KTLLMFDFFHDVAEKAKAGNAKAKEVIQSWADAEWFTTRPEVPKSITVTVFKVPGETNTD 180 Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNARE--GIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238 DLSPAPDAWSRPDIP+H AMLKN R +P++ G GP++ IE L+KKG+ +AYVGD Sbjct: 181 DLSPAPDAWSRPDIPMHYLAMLKNTRPDAAFKPEEDGKRGPMQFIEDLKKKGHLVAYVGD 240 Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298 VVGTGSSRKSATNSV+W G DIP VPNKR GG+ LGGKIAPIFFNT ED+G+LPIEVDV Sbjct: 241 VVGTGSSRKSATNSVIWATGQDIPFVPNKRFGGVTLGGKIAPIFFNTQEDSGSLPIEVDV 300 Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358 S L MGDVI+V PY G++ + G +A F LK++VL+DEVRAGGRI LIIGR LT KAR Sbjct: 301 SKLEMGDVIEVLPYDGKIT--KDGATVAEFALKSEVLLDEVRAGGRINLIIGRSLTGKAR 358 Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415 E LGLP S +FR K +S +GFSLAQKMVGRA G+ +G+RPG YCEPKMT+VGSQD Sbjct: 359 EFLGLPASTLFRLPKAPVDSGKGFSLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQD 418 Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPG 475 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV TH LP FI NRGGV+LRPG Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHRELPAFISNRGGVALRPG 478 Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535 DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAF AATGVMPLDMPESVLVR Sbjct: 479 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFGAATGVMPLDMPESVLVR 538 Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595 F GKMQPGITLRDLVHAIPLYAIK GLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL Sbjct: 539 FSGKMQPGITLRDLVHAIPLYAIKAGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 598 Query: 596 TDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655 +DASAERSAAGC IKLNKEPI EYL SNIVL+K MIA+GY D+RTLERRI+ +E WLA+P Sbjct: 599 SDASAERSAAGCAIKLNKEPIAEYLKSNIVLMKNMIADGYQDKRTLERRIKSVEAWLANP 658 Query: 656 QLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIG 715 QLLEADADAEYAAVI+I+L DIKEPILCAPNDPDDARLLSDV G KIDEVFIGSCMTNIG Sbjct: 659 QLLEADADAEYAAVIEINLDDIKEPILCAPNDPDDARLLSDVAGTKIDEVFIGSCMTNIG 718 Query: 716 HFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775 HFRAA KLL K +P +LWVAPPT+MDAA+LT+EG+Y+VFG +GAR E+PGCSLCMGN Sbjct: 719 HFRAASKLLGGQK-DIPVKLWVAPPTKMDAAELTKEGHYNVFGTAGARTEMPGCSLCMGN 777 Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835 QA+V GATVVSTSTRNFPNRLG NVFLASAELA++A+ +GKLPT EY Y+ ++ Sbjct: 778 QAQVRTGATVVSTSTRNFPNRLGKDTNVFLASAELASIASKLGKLPTVAEYNEYIGVINA 837 Query: 836 TAVDTYRYLNFDQLSQYTEKADGV 859 A + YRY+NFDQ+++Y + A V Sbjct: 838 DAANIYRYMNFDQIAEYADVAKTV 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: 2070 Number of extensions: 83 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: 865 Length of database: 863 Length adjustment: 42 Effective length of query: 823 Effective length of database: 821 Effective search space: 675683 Effective search space used: 675683 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 Sep 24 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