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 GFF3491 HP15_3433 aconitate hydratase 1
Query= SwissProt::P37032 (891 letters) >FitnessBrowser__Marino:GFF3491 Length = 919 Score = 1204 bits (3116), Expect = 0.0 Identities = 602/913 (65%), Positives = 717/913 (78%), Gaps = 29/913 (3%) Query: 3 VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62 + +DSL+T S L GKT++YYSL +A + +NRLP+SLKVL+ENLLR EDG TV Sbjct: 6 LSKDSLNTLSSLDAGGKTFHYYSLPKAADT-LGDLNRLPFSLKVLMENLLRNEDGTTVDR 64 Query: 63 KDIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPL 122 I A+ W+ ++ S EI FRP RVLMQDFTGVP VVDLAAMR A+ G + I+PL Sbjct: 65 SHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPL 124 Query: 123 SPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGIC 182 SPVDLVIDHSVMVDKF A + + N IE+ERN+ERYEFLRWGQ+AF NF+VVPPGTGIC Sbjct: 125 SPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGIC 184 Query: 183 HQVNLEYLGKTVWNSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242 HQVNLEYLGKTVW + DG+ AYPDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQ Sbjct: 185 HQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQ 244 Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302 PVSMLIPEV+GFK++GKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYG GL D+P+ADR Sbjct: 245 PVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADR 304 Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362 ATI+NMAPEYGATCGFFPVD++TIKY+ LTGR++ + LVEAYAKAQG+W + +E PV+ Sbjct: 305 ATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHE-PVY 363 Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNK---- 418 TD+L LD+G VE SLAGPKRPQD+V L ++ F L+E + + + ++++ Sbjct: 364 TDNLELDMGEVEASLAGPKRPQDRVALKNMKSSFE-LLMETAEGPAENREANLESEGGQT 422 Query: 419 ----DFQMKH-----------------GHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEK 457 D KH G VVIAAITSCTNTSNPSV+MAAGL+A+KA++K Sbjct: 423 AVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQK 482 Query: 458 GLQRKPWVKSSLAPGSKVVTDYLRHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISH 517 GL KPWVK+SLAPGSKVVTDYL+ G Q LD+LGFNLVGYGCTTCIGNSGPLPD + Sbjct: 483 GLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEK 542 Query: 518 CVAEHDLVVSSVLSGNRNFEGRVHPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDK 577 +++ DL V+SVLSGNRNFEGRVHP V+ NWLASPPLVVAYAL G DLS++P+G DK Sbjct: 543 AISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDK 602 Query: 578 EGNDVYLKDIWPSNEEIAAEVAKVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDS 637 +GN VYLKD+WPS +EIA V KV MFRKEYAEVF GDA W++I+ + YEW+ S Sbjct: 603 DGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKS 662 Query: 638 TYIQHPPFFENLSLKPEPLKPIKQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKG 697 TYIQHPPFFE L +P+ + IK A +LAL GDS+TTDHISPAGS K +PAG YL+ G Sbjct: 663 TYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHG 722 Query: 698 VDEKDFNSYGSRRGNHEVMMRGTFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRY 757 V+ KDFNSYGSRRGNHEVMMRGTFAN+RIRNEM G EGG T++VPTGE M+IYDAAM+Y Sbjct: 723 VEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKY 782 Query: 758 QENQQDLVIIAGKEYGTGSSRDWAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFK 817 QE LV+IAGKEYGTGSSRDWAAKGT LLGVKAV+ ES+ERIHRSNLIGMG++PLQF Sbjct: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842 Query: 818 EGTTRKTLKLDGSERISIE-ISDKLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYY 876 EGT RK+LKL G E ISIE +S ++ PG + +T++ +DG E E RIDTA+E Y+ Sbjct: 843 EGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902 Query: 877 KNGGILQYVLRKI 889 K+GGIL YV+R++ Sbjct: 903 KHGGILHYVVREM 915 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: 2253 Number of extensions: 99 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: 891 Length of database: 919 Length adjustment: 43 Effective length of query: 848 Effective length of database: 876 Effective search space: 742848 Effective search space used: 742848 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 17 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