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 AO356_02385 AO356_02385 aconitate hydratase
Query= SwissProt::Q8ZP52 (891 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02385 Length = 913 Score = 1253 bits (3241), Expect = 0.0 Identities = 617/900 (68%), Positives = 728/900 (80%), Gaps = 21/900 (2%) Query: 12 TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71 TLQ +TYHY+SLP AA+SLGD+ +LP SLKVLLENLLRW+D ++VT D++ALAGWLK Sbjct: 12 TLQVDARTYHYFSLPDAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAGWLK 71 Query: 72 NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131 +DREI +RPARVLMQDFTGVPAVVDLAAMR AV++ GGD ++NPLSPVDLVIDHSV Sbjct: 72 ERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSPVDLVIDHSV 131 Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191 VD F AFE+NV +EM+RN ERY FL+WG+ AF FSVVPPGTGICHQVNLEYLG+ Sbjct: 132 MVDKFASSQAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRT 191 Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251 VW++ +DG A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G Sbjct: 192 VWTKEEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251 Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311 FKL GKLREGITATDLVLTVTQMLRK GVVGKFVEFYGDGL LPLADRATIANM+PEYG Sbjct: 252 FKLIGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYG 311 Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371 ATCGFFP+D +TL+Y+RLSGR + V+LVE Y KAQG+WR PG EPVFT TLELDMG VE Sbjct: 312 ATCGFFPVDEVTLDYLRLSGRPAETVKLVEAYCKAQGLWRLPGQEPVFTDTLELDMGSVE 371 Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPVD------------------- 412 ASLAGPKRPQDRV+L +V +AF+ L++ ++ ++ Sbjct: 372 ASLAGPKRPQDRVSLPNVGQAFSDFLGLQVKPTSKEEGRLESEGGGGVAVGNADQVGEAE 431 Query: 413 YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPG 472 Y G ++L +GAVVIAAITSCTNTSNPSV+MAAGLLAKKAV GL R+PWVK+SLAPG Sbjct: 432 YEFEGHTHRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLVRKPWVKSSLAPG 491 Query: 473 SKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSG 532 SKVV+DY A LT YLD+LGF+LVGYGCTTCIGNSGPLP+PIE AI+K DLTV +VLSG Sbjct: 492 SKVVTDYYNAAGLTEYLDKLGFDLVGYGCTTCIGNSGPLPDPIEKAIQKADLTVASVLSG 551 Query: 533 NRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQ 592 NRNFEGR+HPLVKTNWLASPPLVVAYALAG + I+++++PLG DR G PVYL+DIWPS+Q Sbjct: 552 NRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGKPVYLRDIWPSSQ 611 Query: 593 EIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQ 652 E+A AV V++ MF KEYA VF G E+W++I+V + TY WQ DSTYI+ PFFD++ Sbjct: 612 EVAAAVAQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYIQHPPFFDDIGGP 671 Query: 653 PAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGN 712 P V+++ GAR+LA+LGDSVTTDHISPAG+IK DSPAGRYL+ GVE +DFNSYGSRRGN Sbjct: 672 PPAVRNVEGARVLALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGN 731 Query: 713 HEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEY 772 H+VMMRGTFANIRIRNEML G EGG T ++P E M IYDAAMLYQ TPL VIAG+EY Sbjct: 732 HQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAAMLYQATDTPLVVIAGQEY 791 Query: 773 GSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEV 832 G+GSSRDWAAKG LLG++ VIAESFERIHRSNL+GMG+LPL+F RK+L LTG E Sbjct: 792 GTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGRET 851 Query: 833 IDIADLQN--LRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890 +DI L + L P +P+ +TR DG +E + CRIDT E+ Y++ GILHYV+R ++ Sbjct: 852 LDILGLNDVELTPRMNLPLVITREDGRQERIEVLCRIDTLNEVEYFKAGGILHYVLRQLI 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: 2231 Number of extensions: 95 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: 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