Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate Ac3H11_3150 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3150 Length = 866 Score = 126 bits (317), Expect = 2e-33 Identities = 127/453 (28%), Positives = 211/453 (46%), Gaps = 46/453 (10%) Query: 2 TLVEKILSKKVGYE----VCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIV 57 TL +K++ + VG V G E ++ + D T P+ LK+++ ++ D ++ Sbjct: 383 TLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVM 442 Query: 58 VAFDHNVP-PNTVKAAEMQKLALEFVKRFGIKNFHKGGEGICHQILAENYVLPNMFVAGG 116 +F H P V ++L R G+ + G+G+ H L +LP+ GG Sbjct: 443 QSFCHTAAYPKPVDVKTHRELPAFISNRGGVAL--RPGDGVIHSWL-NRLLLPDTVGTGG 499 Query: 117 DSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NVSAKDIVLRV 175 DSHT +F G G +A+ ATG + +P++I V G + V+ +D+V + Sbjct: 500 DSHTRFPIGI-SFPAGSGL--VAFGAATGVMPLDMPESILVRFKGDMQPGVTLRDLVHAI 556 Query: 176 CKEIGRRGATYMAIE-----YGGEVVK-----NMDMDGRLTLCNMAIEMGGKTGVIEAD- 224 + G +A + G +++ ++ ++ L + + E I+ + Sbjct: 557 PLYAIKAGLLTVAKAGKINAFSGRILEIEGLPDLKVEQAFELSDASAERSAAGCTIKLNP 616 Query: 225 EITYDYLKKERGLSDEDIAKLKKERITVNR------------------DEANYYKEIEID 266 E +YL L IA + T+ R +A Y IEID Sbjct: 617 EPIKEYLTSNIVLMKNMIADGYADAKTLQRRIEKVEAWLAKPDLLEADKDAEYAAVIEID 676 Query: 267 ITDMEEQ-VAVPHHPDNVKPISDVEGTEINQVFIGSCTNGRLSDLREAAKYLKGREVHKD 325 + D++E V P+ PD+ K +S+V GT+I++ FIGSC + R AAK L G+ Sbjct: 677 LADIKEPIVCCPNDPDDAKFLSEVSGTKIDEAFIGSCMT-NIGHFRAAAKLLGGQR-DIP 734 Query: 326 VKLIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNR 385 VKL V P +K + +KEG F AGA PGC C+G +Q + EG +ST+ R Sbjct: 735 VKLWVAPPTKMDESELIKEGHYAAFGTAGARTEMPGCSLCMG-NQAQVREGATVISTSTR 793 Query: 386 NFKGRMGHINSYIYLASPKIAAISAVKGYITNK 418 NF R+G N+ ++L S ++AAI++ GY+ +K Sbjct: 794 NFPNRLGK-NTNVFLGSAELAAIASRLGYLPSK 825 Lambda K H 0.318 0.136 0.399 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: 800 Number of extensions: 44 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 420 Length of database: 866 Length adjustment: 37 Effective length of query: 383 Effective length of database: 829 Effective search space: 317507 Effective search space used: 317507 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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