Align Aconitate hydratase A; 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 BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1
Query= SwissProt::Q8ZP52 (891 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1 Length = 890 Score = 1594 bits (4128), Expect = 0.0 Identities = 781/890 (87%), Positives = 842/890 (94%) Query: 1 MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTD 60 MSSTLR ASKDTLQ KDKT+HYYSLPLAAK LGD++RLPKSLKVLLENLLRWQDG+SVT Sbjct: 1 MSSTLRAASKDTLQVKDKTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTA 60 Query: 61 EDIQALAGWLKNAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPL 120 EDI ALAGWLK+AHADREIA+RPARVLMQDFTGVPAVVDLAAMREAVKRLGGDT+KVNPL Sbjct: 61 EDIHALAGWLKHAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120 Query: 121 SPVDLVIDHSVTVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGIC 180 SPVDLVIDHSVTVD FGDDDAFEENVRLEMERNHERY+FL+WG+QAFSRFSVVPPGTGIC Sbjct: 121 SPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVFLRWGQQAFSRFSVVPPGTGIC 180 Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240 HQVNLEYLG+AVWSE Q+GEW+A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ Sbjct: 181 HQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240 Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300 PVSMLIPDVVGFKL+GKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR Sbjct: 241 PVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300 Query: 301 ATIANMSPEYGATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFT 360 ATIANMSPEYGATCGFFPIDA+TL+YMRL+GRS++ V LVE YAKAQGMWR PGDEPVFT Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFT 360 Query: 361 STLELDMGDVEASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPVDYTMNGQPY 420 STL LDMG VEASLAGPKRPQDRVALGDVP+AFAAS+ELE+N AQ+D++P+DYT+NGQ Y Sbjct: 361 STLALDMGTVEASLAGPKRPQDRVALGDVPQAFAASSELEVNHAQKDKRPIDYTLNGQQY 420 Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480 LPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAV GLK QPWVKASLAPGSKVVSDYL Sbjct: 421 SLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYL 480 Query: 481 AQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSGNRNFEGRI 540 A AKLTP+LDELGFNLVGYGCTTCIGNSGPLP+PIE AIK+GDLTVGAVLSGNRNFEGRI Sbjct: 481 AHAKLTPWLDELGFNLVGYGCTTCIGNSGPLPDPIERAIKQGDLTVGAVLSGNRNFEGRI 540 Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQEIARAVEL 600 HPLVKTNWLASPPLVVAYALAGNMN++L +PLG + G PVYLKDIWPS E+A+AVE Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQPVYLKDIWPSGIEVAQAVEQ 600 Query: 601 VSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQPAPVKDIH 660 VS++MFRKEYAEVFEGT EWK+I+V+ SDTY WQ+DSTYIRLSPFFDEM +P PV+DIH Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGVEPKPVEDIH 660 Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGNHEVMMRGT 720 GARILAMLGDSVTTDHISPAGSIK DSPAGRYLQNHGVER DFNSYGSRRGNHEVMMRGT Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGT 720 Query: 721 FANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEYGSGSSRDW 780 FANIRIRNEM+PGVEGGMTRHLP T+ ++IYDAAMLY++E TPLAVIAGKEYGSGSSRDW Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDW 780 Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEVIDIADLQN 840 AAKGPRLLG+RVVIAESFERIHRSNLIGMGILPLEFPQG+TRKTLGL GEE IDI++LQ Sbjct: 781 AAKGPRLLGVRVVIAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQA 840 Query: 841 LRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890 L+PG T+PVTLTR+DG +E + CRCRIDTATELTYYQNDGILHYVIRNML Sbjct: 841 LQPGMTVPVTLTRADGRQEVIDCRCRIDTATELTYYQNDGILHYVIRNML 890 Lambda K H 0.317 0.135 0.401 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: 2468 Number of extensions: 100 Number of successful extensions: 2 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: 890 Length adjustment: 43 Effective length of query: 848 Effective length of database: 847 Effective search space: 718256 Effective search space used: 718256 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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