Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_099019639.1 CCS90_RS11175 aconitate hydratase AcnA
Query= SwissProt::P37032 (891 letters) >NCBI__GCF_002591915.1:WP_099019639.1 Length = 887 Score = 1057 bits (2733), Expect = 0.0 Identities = 518/889 (58%), Positives = 672/889 (75%), Gaps = 7/889 (0%) Query: 6 DSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTKDI 65 D+L T QL + K+Y Y+SL + H I+RLP+SLK+LLENLLR E+G VT DI Sbjct: 3 DTLKTAMQLACNNKSYKYFSLAKIAETH--DISRLPFSLKILLENLLRNENGIDVTVSDI 60 Query: 66 KAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLSPV 125 +A+ +W N EIAF P+RV++QDFTGVPAVVDLAAMR A+ +GG+ KI+PLSP Sbjct: 61 EALCNWDPNAAPATEIAFTPSRVVLQDFTGVPAVVDLAAMRDAMKALGGDVQKINPLSPA 120 Query: 126 DLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICHQV 185 +LVIDHS+ VDK+ + D+ E+NT+IE +RN ERY FL+WGQ AF F+VVPPG GI HQV Sbjct: 121 ELVIDHSIQVDKYGTMDSAEINTQIEFQRNMERYGFLKWGQTAFDTFKVVPPGNGIVHQV 180 Query: 186 NLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVS 245 NLEYL + ++ +E +G+L AYPDT+VGTDSHTTMING+GVLGWGVGGIEAEAAMLGQ +S Sbjct: 181 NLEYLARVIFGAEKNGELMAYPDTVVGTDSHTTMINGIGVLGWGVGGIEAEAAMLGQAIS 240 Query: 246 MLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADRATI 305 MLIP+V+GFKL+GK++EG+TATDLVLTV MLR+ GVVGKFVEF+G GL LPLADRATI Sbjct: 241 MLIPQVVGFKLTGKMQEGVTATDLVLTVVDMLREHGVVGKFVEFFGSGLQHLPLADRATI 300 Query: 306 SNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVFTDS 365 +NMAPEYGATCG FP+D E+++YL L+GR + + LVEAYAKAQGM++D+++ + +T Sbjct: 301 ANMAPEYGATCGIFPIDNESLRYLTLSGRSEEQVNLVEAYAKAQGMFHDENSIDAEYTAV 360 Query: 366 LHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNK--DFQMK 423 L LD+ +V PS++GPKRPQD++ L+ +N E + K+ AV + ++ Sbjct: 361 LELDMSTVVPSISGPKRPQDRIELTVAKETYNRHFKEF-ENGRAVKSVAVSSDRGNYDFT 419 Query: 424 HGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRHA 483 G++ +AAITSCTNTSNP+V++ AGL+A+ A KGL+ KPWVK+SLAPGSKVV+ YL A Sbjct: 420 DGNIAVAAITSCTNTSNPAVMLGAGLLARNAAAKGLKVKPWVKTSLAPGSKVVSHYLNAA 479 Query: 484 GLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHPQ 543 G+ L+ LGFN+VG+GCTTCIGNSGPL +S + ++DL+ +SVLSGNRNFEGR+H Sbjct: 480 GVMDDLETLGFNVVGFGCTTCIGNSGPLDPALSKAINDNDLIATSVLSGNRNFEGRIHAD 539 Query: 544 VRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEVA-KVS 602 ++ N+LASPPLVVAYA+ GT DL + +G+D+EGN VYL+DIWPSN EIA + VS Sbjct: 540 IQMNFLASPPLVVAYAIAGTMDFDLQNDSLGEDQEGNPVYLRDIWPSNHEIADTIQNNVS 599 Query: 603 GTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQA 662 T F + Y +F+GDA+WQA++T+ + ++W DSTYI++PP+F+ ++L+ + I A Sbjct: 600 KTSFSEGYEGIFEGDANWQAVKTTESELFDWQGDSTYIKNPPYFDGMTLEVGTIDNISGA 659 Query: 663 YVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTFA 722 VLA GDS+TTDHISPAG+I SPAG YLK KGV + +FNSYGSRRGNHEVMMRGTFA Sbjct: 660 RVLAKLGDSVTTDHISPAGAIAEDSPAGSYLKEKGVPKVNFNSYGSRRGNHEVMMRGTFA 719 Query: 723 NIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWAA 782 NIR+RN++ PG EGG TR+ P+ E MSI+DA+M+YQ L++I G EYGTGSSRDWAA Sbjct: 720 NIRLRNQLAPGTEGGWTRHQPSNEEMSIFDASMKYQAEGTPLLVIGGTEYGTGSSRDWAA 779 Query: 783 KGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISDKLT 842 KGTNLLGVKAV+ +S+ERIHRSNL+GMG++PLQFK G + T L G E + K Sbjct: 780 KGTNLLGVKAVLVQSYERIHRSNLVGMGVIPLQFKAGESADTYDLTGKEVYDVS-GLKNG 838 Query: 843 PGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKISS 891 +T+ R+DG E RIDT E+EY ++GGIL YVLR ++S Sbjct: 839 ESKTAQITVHREDGSTVSFEVDVRIDTPKEVEYCRHGGILHYVLRNLAS 887 Lambda K H 0.316 0.134 0.393 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: 2028 Number of extensions: 95 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: 891 Length of database: 887 Length adjustment: 43 Effective length of query: 848 Effective length of database: 844 Effective search space: 715712 Effective search space used: 715712 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