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 AO353_00565 AO353_00565 aconitate hydratase
Query= SwissProt::Q8ZP52 (891 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00565 Length = 916 Score = 1228 bits (3178), Expect = 0.0 Identities = 613/903 (67%), Positives = 718/903 (79%), Gaps = 24/903 (2%) Query: 12 TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71 TL+ DKTYHY+SLP AAKSLGD+ +LP SLKVLLENLLRW+D ++VT D++ALA WLK Sbjct: 12 TLKIDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLK 71 Query: 72 NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131 +DREI +RPARVLMQDFTGVPAVVDLAAMR A+ + GGD ++NPLSPVDLVIDHSV Sbjct: 72 ERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSV 131 Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191 VD F AF +NV +EM+RN ERY FL+WG+ AF FSVVPPGTGICHQVNLEYLG+ Sbjct: 132 MVDKFASSTAFTQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRT 191 Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251 VW++ +D A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G Sbjct: 192 VWTKDEDDRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251 Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311 FKLTGKL+EGITATDLVLTVTQMLRK GVVGKFVEFYGDGL LPLADRATIANM+PEYG Sbjct: 252 FKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYG 311 Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371 ATCGFFP+D +TLEY+RLSGR +V+LVE Y K QG+WR PG EPVFT +L LDM VE Sbjct: 312 ATCGFFPVDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDSLALDMSSVE 371 Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQP--------------------- 410 ASLAGPKRPQDRV+L +V +AF L++ A+ + Sbjct: 372 ASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGVAVGNADLVS 431 Query: 411 -VDYTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASL 469 DY GQ Y+L +GAVVIAAITSCTNTSNPSV+MAAGL+AKKAV GLKR+PWVK+SL Sbjct: 432 EADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSL 491 Query: 470 APGSKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAV 529 APGSKVV+DY A LT YLDELGF+LVGYGCTTCIGNSGPL EPIE AI+ DL V +V Sbjct: 492 APGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEKAIQSSDLAVASV 551 Query: 530 LSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWP 589 LSGNRNFEGR+HPLVKTNWLASPPLVVAYALAG++ ++++++PLG + G PVYL+DIWP Sbjct: 552 LSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGKPVYLRDIWP 611 Query: 590 SAQEIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEM 649 S++EIA AV V + MF KEYAEVF G +W++I+V + TY WQ DSTYI+ PFFD++ Sbjct: 612 SSKEIADAVAQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPPFFDDI 671 Query: 650 QAQPAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSR 709 ++DI GARILA+LGDSVTTDHISPAG+IK DSPAGRYL+ GVE +DFNSYGSR Sbjct: 672 SGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSR 731 Query: 710 RGNHEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAG 769 RGNHEVMMRGTFANIRIRNEML G EGG T ++P E ++IYDAAM YQ TPL VIAG Sbjct: 732 RGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRYQAAGTPLVVIAG 791 Query: 770 KEYGSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTG 829 +EYG+GSSRDWAAKG LLG++ VIAESFERIHRSNL+GMG+LPL+F RK+L LTG Sbjct: 792 QEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTG 851 Query: 830 EEVIDIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIR 887 +E +DI L L P + + +TR DGS E V CRIDT E+ Y++ GILHYV+R Sbjct: 852 KETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLR 911 Query: 888 NML 890 ++ Sbjct: 912 QLI 914 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: 2201 Number of extensions: 89 Number of successful extensions: 3 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: 916 Length adjustment: 43 Effective length of query: 848 Effective length of database: 873 Effective search space: 740304 Effective search space used: 740304 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