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 Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
Query= SwissProt::Q8ZP52 (891 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Length = 913 Score = 1241 bits (3211), Expect = 0.0 Identities = 614/900 (68%), Positives = 723/900 (80%), Gaps = 21/900 (2%) Query: 12 TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71 TLQ DKTYHY+SLP AAKSLGD+ +LP SLKVLLENLLRW+D ++VT D++A+A WLK Sbjct: 12 TLQVDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKAIAAWLK 71 Query: 72 NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131 +DREI +RPARVLMQDFTGVPAVVDLAAMR A+ + GGD ++NPLSPVDLVIDHSV Sbjct: 72 ERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSV 131 Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191 VD + AF +NV +EM+RNHERY FL+WG+ AF+ FSVVPPGTGICHQVNLEYLG+ Sbjct: 132 MVDKYASASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRT 191 Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251 VW++ +DG A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G Sbjct: 192 VWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251 Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311 FKLTGKL+EGITATDLVLTVTQMLRK GVVGKFVEFYGDGL LPLADRATIANM+PEYG Sbjct: 252 FKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYG 311 Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371 ATCGFFP+D +TLEY+RLSGR+ V+LVE Y+K QG+WR PG EPVFT +L LDMG VE Sbjct: 312 ATCGFFPVDEVTLEYLRLSGRTPQTVKLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVE 371 Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPV-------------------D 412 ASLAGPKRPQDRV+L +V +AF L+ + ++ + D Sbjct: 372 ASLAGPKRPQDRVSLPNVAQAFTDFLGLQFKPSSKEEGRLESEGGGGVAVGNADLIGEAD 431 Query: 413 YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPG 472 Y G Y+L +GAVVIAAITSCTNTSNPSV+MAAGL+AKKAV GLKR+PWVK+SLAPG Sbjct: 432 YHHEGSTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPG 491 Query: 473 SKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSG 532 SKVV+DY A LT YLDELGF LVGYGCTTCIGNSGPLPEPIE AI+K DLTV +VLSG Sbjct: 492 SKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSG 551 Query: 533 NRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQ 592 NRNFEGR+HPLVKTNWLASPPLVVAYALAG + I+++++PLG D+ G PVYL+DIWPS + Sbjct: 552 NRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDKDGHPVYLRDIWPSTK 611 Query: 593 EIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQ 652 EIA AV V++ MF KEYAEVF G E+W++I+V + TY W +DSTYI+ PFFD++ Sbjct: 612 EIADAVTQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDSTYIQHPPFFDDIGGP 671 Query: 653 PAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGN 712 VKD+ GA++LA+LGDSVTTDHISPAG+IK DSPAG YL+ GVE +DFNSYGSRRGN Sbjct: 672 APVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPRDFNSYGSRRGN 731 Query: 713 HEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEY 772 H+VMMRGTFANIRIRNEML G EGG T ++P E + IYDAAM YQ TPL VIAG+EY Sbjct: 732 HQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMRYQASGTPLVVIAGQEY 791 Query: 773 GSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEV 832 G+GSSRDWAAKG LLG++ VIAESFERIHRSNL+GMG+LPL+F RK+L LTG+E Sbjct: 792 GTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKET 851 Query: 833 IDIADLQ--NLRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890 +DI L L P + + +TR DG+ E V CRIDT E+ Y++ GILHYV+R ++ Sbjct: 852 LDILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 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: 2211 Number of extensions: 94 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