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_008343808.1 BA79_RS03665 aconitate hydratase AcnA
Query= SwissProt::Q5SMF6 (902 letters) >NCBI__GCF_000691145.1:WP_008343808.1 Length = 909 Score = 1074 bits (2777), Expect = 0.0 Identities = 535/898 (59%), Positives = 672/898 (74%), Gaps = 5/898 (0%) Query: 2 KNSFQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTRED 61 +++FQ+ KT +T TY YY L+ LE++G+ VS+LP+SI+V+LES+LR DG + +E Sbjct: 10 QDAFQSRKTFSTNGKTYHYYSLEALEKQGIGNVSKLPYSIKVLLESVLRQVDGRVIKKEH 69 Query: 62 IEALARW-RPDPGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVP 120 +E LA+W + EI+VP K +RVILQDFTGVPAVVDLA++R A+ GGDP +INP +P Sbjct: 70 VENLAKWGTAEVKEIDVPFKPSRVILQDFTGVPAVVDLASLRKAMADVGGDPDKINPEIP 129 Query: 121 ADLVIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQ 180 DLVIDHSVQVD GT A N++ E+ERN ERY L WA+ A N++ VPP TGIVHQ Sbjct: 130 VDLVIDHSVQVDKAGTEDALNINMDLEFERNAERYNFLSWAKKAFNNYQAVPPATGIVHQ 189 Query: 181 VNIEYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPY 240 VN+EYL VV + DG + +PD+LVGTDSHTTM+NG+GVLGWGVGGIEAEA MLGQP Sbjct: 190 VNLEYLASVVHAIEEDGEIITYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLGQPS 249 Query: 241 YMLAPRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRAT 300 Y P V+G KL GELP G TATDL L VT++LR+ GVV KFVEF+GPGVA+L DRAT Sbjct: 250 YFPVPEVIGAKLVGELPNGTTATDLALKVTQVLREKGVVNKFVEFFGPGVAQLPLADRAT 309 Query: 301 IANMAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYS 360 IANMAPEYGAT GFFPVDEE L YLR TGR EE + +VE Y++A GLF TP+AEE + ++ Sbjct: 310 IANMAPEYGATCGFFPVDEEALAYLRLTGRDEEQINIVEEYSRANGLFYTPDAEEPI-FT 368 Query: 361 EYLELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKV-LV 419 + +E+DLS +E +L+GPKRPQD +PL ++K++F H+ P +GFGL + +L +++ Sbjct: 369 DVVEIDLSQIESNLSGPKRPQDLIPLSQMKETFHKHIESPAGNQGFGLEKSELDKQIEFD 428 Query: 420 KRRDEEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGS 479 E+ + G++ IAAITSCTNTSNP V++GAGL+AKKA E G+ +VKTSLAPGS Sbjct: 429 LANGEKAVMKTGAIAIAAITSCTNTSNPYVLIGAGLVAKKASELGMKVPNYVKTSLAPGS 488 Query: 480 KVVTDYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGN 539 KVVT YL SGL+P+L LGF++VGYGCTTCIGNSGPL ++I AV E +L++ +VLSGN Sbjct: 489 KVVTGYLVNSGLLPYLRDLGFNIVGYGCTTCIGNSGPLEKEIEDAVSENDLLITSVLSGN 548 Query: 540 RNFEGRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEE 599 RNFEGRI+P VK NYLASP LVVAYALAG ++ID T +P+G D NG+ +Y DIWPSM+E Sbjct: 549 RNFEGRIHPLVKGNYLASPPLVVAYALAGTVNIDLTKDPIGVDKNGENVYFNDIWPSMDE 608 Query: 600 IREAIRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER 659 I ++ T+ PELF+ EY VF+ ++RW + LY+WD STYI NPPFFE+L Sbjct: 609 INSVVKSTVTPELFRSEYETVFDNNDRWNEIKTTDDALYKWDENSTYIDNPPFFENLSVE 668 Query: 660 --KVEDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGN 717 KVE ++G RV+ GDSVTTDHISPAGAI +PAG+YL +GV P DFNSYGSRRGN Sbjct: 669 PGKVEPLKGLRVVAKFGDSVTTDHISPAGAIGKDTPAGKYLQERGVSPRDFNSYGSRRGN 728 Query: 718 HEVMMRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEY 777 H VMMRGTFANIRIKN + G EGGY P G+V +Y+ MRYK +GT L ++AGK+Y Sbjct: 729 HHVMMRGTFANIRIKNQIAPGTEGGYTTYWPTGEVTSIYDACMRYKEDGTGLAILAGKDY 788 Query: 778 GTGSSRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEV 837 G GSSRDWAAKGT LLGI+ VLAESFERIHRSNLV MGVLPL+F GE+ ET GLTG E Sbjct: 789 GMGSSRDWAAKGTNLLGIKFVLAESFERIHRSNLVFMGVLPLQFKDGESAETYGLTGTET 848 Query: 838 YDILGLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895 +++ E ++PR LV + A DG+E F+ I R D+ VE+DYY++GGILQ VL L Sbjct: 849 FEVDVDETVRPRDLVTVKAIDTDGNEKTFEVIVRFDSEVEIDYYRHGGILQMVLREKL 906 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: 2188 Number of extensions: 112 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: 902 Length of database: 909 Length adjustment: 43 Effective length of query: 859 Effective length of database: 866 Effective search space: 743894 Effective search space used: 743894 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