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 PP_2112 PP_2112 aconitate hydratase 1
Query= SwissProt::Q8ZP52 (891 letters) >FitnessBrowser__Putida:PP_2112 Length = 913 Score = 1252 bits (3239), Expect = 0.0 Identities = 621/899 (69%), Positives = 720/899 (80%), Gaps = 21/899 (2%) Query: 13 LQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLKN 72 L+ DKTYHY+SL AA+ LGD+ RLP SLKVLLENLLRW+DG +VT +D++A+A WL Sbjct: 13 LKVGDKTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDDLRAIAQWLGE 72 Query: 73 AHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSVT 132 +DREI +RPARVLMQDFTGVPAVVDLAAMR A+ + GGD ++NPLSPVDLVIDHSV Sbjct: 73 RRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVM 132 Query: 133 VDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKAV 192 VD +G AF ENV +EM+RN ERY FL+WG+ AF F VVPPGTGICHQVNLEYLG+ V Sbjct: 133 VDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQVNLEYLGRTV 192 Query: 193 WSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGF 252 W+ DG A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+GF Sbjct: 193 WTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGF 252 Query: 253 KLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYGA 312 KLTGKLREGITATDLVLTVTQMLRK GVVGKFVEFYGDGL LPLADRATIANM+PEYGA Sbjct: 253 KLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGA 312 Query: 313 TCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVEA 372 TCGFFP+D +TL+Y+RLSGR + V+LVE Y KAQGMWR PG EP F+ TL LDM DVEA Sbjct: 313 TCGFFPVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDTLALDMDDVEA 372 Query: 373 SLAGPKRPQDRVALGDVPKAFAASAELELNTAQRD-------------------RQPVDY 413 SLAGPKRPQDRVALG V +AF EL+ ++ VDY Sbjct: 373 SLAGPKRPQDRVALGQVSQAFDHFIELQPKPLAKEVGRLESEGGGGVAVGNADQTGAVDY 432 Query: 414 TMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGS 473 + GQ + L DGAVVIAAITSCTNTSNPSV+MAAGL+AKKA+ GL+R+PWVK+SLAPGS Sbjct: 433 SHQGQTHTLRDGAVVIAAITSCTNTSNPSVMMAAGLVAKKALEKGLQRKPWVKSSLAPGS 492 Query: 474 KVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSGN 533 KVV+DY A LTPYLD+LGF+LVGYGCTTCIGNSGPL E IE AI DLTV +VLSGN Sbjct: 493 KVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAIEKAIGSADLTVASVLSGN 552 Query: 534 RNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQE 593 RNFEGR+HPLVKTNWLASPPLVVAYALAG++ ++L DPLG + G PVYL+DIWPS QE Sbjct: 553 RNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGSGKDGQPVYLRDIWPSQQE 612 Query: 594 IARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQP 653 IA AV V + MF KEYAEVF G +W++I+V + TY WQ+DSTYI+ PFFD + P Sbjct: 613 IAEAVAKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQADSTYIQHPPFFDGIGGPP 672 Query: 654 APVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGNH 713 + +IHGAR+LA+LGDSVTTDHISPAG+IK DSPAGRYL+ GVE +DFNSYGSRRGNH Sbjct: 673 PQIANIHGARVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNH 732 Query: 714 EVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEYG 773 EVMMRGTFANIRIRNEML G EGG T H+P E +SIYDAAM YQQE TPL VIAG+EYG Sbjct: 733 EVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEKLSIYDAAMRYQQEGTPLLVIAGQEYG 792 Query: 774 SGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEVI 833 +GSSRDWAAKG LLG++ V+AESFERIHRSNL+GMG+LPL+F G RK LGLTG+E I Sbjct: 793 TGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQFKAGHNRKQLGLTGKEQI 852 Query: 834 DIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890 D+ L ++ PG ++P+ +TR DG +E + CRIDT E+ Y++ GILHYV+R M+ Sbjct: 853 DVLGLDGAHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEVEYFKAGGILHYVLRQMI 911 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: 2250 Number of extensions: 96 Number of successful extensions: 4 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: 913 Length adjustment: 43 Effective length of query: 848 Effective length of database: 870 Effective search space: 737760 Effective search space used: 737760 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