Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_036833329.1 N784_RS06120 aconitate hydratase AcnA
Query= SwissProt::Q5SMF6 (902 letters) >NCBI__GCF_000775615.1:WP_036833329.1 Length = 904 Score = 1060 bits (2740), Expect = 0.0 Identities = 544/901 (60%), Positives = 673/901 (74%), Gaps = 6/901 (0%) Query: 1 MKNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRE 60 +K++FQ K Y YY L+ LE G+ ++SRLP+SIRV+LES+LR DG + +E Sbjct: 3 VKDTFQAHKQFELNGKKYNYYKLKTLEEAGLGKISRLPYSIRVLLESVLRQHDGEVIQKE 62 Query: 61 DIEALARWRPDPGE-INVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVV 119 IE LA+W E ++VP K +RVILQDFTGVPAVVDLA++R A+ GG P +INP V Sbjct: 63 HIEKLAKWGSKEAESVDVPFKPSRVILQDFTGVPAVVDLASLRKAMVDMGGSPDKINPEV 122 Query: 120 PADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVH 179 P DLVIDHSVQVD +GTA A N+E E+ERN+ERY L WA+ A +N++ VPP TGIVH Sbjct: 123 PVDLVIDHSVQVDEYGTAKALDANMELEFERNKERYEFLNWAKKAFDNYQAVPPATGIVH 182 Query: 180 QVNIEYLTKVVMTGKRD-GLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQ 238 QVN+EYL VV + + G A+PD+LVGTDSHTTM+NGLGVLGWGVGGIEAEA MLGQ Sbjct: 183 QVNLEYLANVVHAIENEKGEYDAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQ 242 Query: 239 PYYMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDR 298 P Y AP V+G KL G LP+G TATDL L VT+ LR+ VVGKFVEF+GPG+ ++ DR Sbjct: 243 PSYFPAPEVIGVKLTGTLPKGTTATDLALKVTQKLREKNVVGKFVEFFGPGLTEMPLADR 302 Query: 299 ATIANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQ 358 ATI+NMAPEYGAT GFFPVD+E+L YLR TGR EE ++LVEAY K LF TP+ E+ Sbjct: 303 ATISNMAPEYGATCGFFPVDQESLEYLRLTGRSEEQIQLVEAYCKENDLFYTPDQEDPT- 361 Query: 359 YSEYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVL 418 +++ +E+ L +EP+L+GPKRPQD +PL E+K+SF LT P +GFGL E + +KV Sbjct: 362 FTDLVEIKLDELEPNLSGPKRPQDLIPLTEMKESFNKALTAPEGNQGFGLDEKEKDKKVS 421 Query: 419 VKRRD-EEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAP 477 V+ + + G+V IAAITSCTNTSNP VMLGAGLLAKKAVE GL+ +VKTSLAP Sbjct: 422 VQHPSGKSSTMKTGAVAIAAITSCTNTSNPYVMLGAGLLAKKAVEKGLEVPEYVKTSLAP 481 Query: 478 GSKVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLS 537 GSKVVT YLE SGLM +LE LGF+ VGYGCTTCIGNSGPL ++ +A+ + +L V++VLS Sbjct: 482 GSKVVTRYLEDSGLMTYLEKLGFNTVGYGCTTCIGNSGPLSPEVEQAIADNDLTVSSVLS 541 Query: 538 GNRNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSM 597 GNRNFEGRI+P VKANYLASP LVVAYALAG +DID E LG D +GK ++ DIWPSM Sbjct: 542 GNRNFEGRIHPLVKANYLASPPLVVAYALAGTVDIDLRKESLGKDHDGKDVHFDDIWPSM 601 Query: 598 EEIREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLG 657 +EI+ + K ++PE+F+KEY VF+ +E+W + LY WD ESTYIQNPPFF L Sbjct: 602 DEIKAEVDKHVNPEIFRKEYEDVFDSNEKWNQIQTTDEPLYNWDDESTYIQNPPFFVGLS 661 Query: 658 E--RKVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRR 715 E +V+D+ G RV+ GDSVTTDHISPAGAI PAG+YL KGV P FNSYGSRR Sbjct: 662 EDPSEVKDLDGLRVIGKFGDSVTTDHISPAGAIAKDMPAGKYLQDKGVSPRHFNSYGSRR 721 Query: 716 GNHEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGK 775 GNHEVMMRGTFANIRI+N + G EGGY P +V +Y+ AM+Y+ +GT LLVIAG Sbjct: 722 GNHEVMMRGTFANIRIRNKIAPGTEGGYTTFWPTDEVMPIYDAAMKYQEQGTGLLVIAGN 781 Query: 776 EYGTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGY 835 +YG GSSRDWAAKGT LLGI+ V+AESFERIHRSNLV MGVLPL+F G++ ++LGL+G Sbjct: 782 DYGMGSSRDWAAKGTNLLGIKTVIAESFERIHRSNLVMMGVLPLQFKDGDSADSLGLSGK 841 Query: 836 EVYDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895 E +DI E +KPR LVD++A E G++ FQ IAR D+ VE+DYY++GGILQ VL + L Sbjct: 842 ETFDIKIDETVKPRDLVDVIAIDEAGNKTEFQVIARFDSGVEIDYYRHGGILQKVLRDKL 901 Query: 896 K 896 + Sbjct: 902 Q 902 Lambda K H 0.317 0.137 0.399 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: 2257 Number of extensions: 104 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: 902 Length of database: 904 Length adjustment: 43 Effective length of query: 859 Effective length of database: 861 Effective search space: 739599 Effective search space used: 739599 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)
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