Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_029000299.1 H537_RS0126670 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P81291 (424 letters) >NCBI__GCF_000430725.1:WP_029000299.1 Length = 863 Score = 125 bits (313), Expect = 7e-33 Identities = 125/460 (27%), Positives = 200/460 (43%), Gaps = 61/460 (13%) Query: 2 GMTIVEKILAKASGKKE---VSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPE 58 G T+ +K++ +A G E + PG + D TGP+T + LK+ ++ + Sbjct: 381 GFTLAQKMVGRACGLPEGQGIRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLG-FSAD 439 Query: 59 KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118 ++ F H + H + +F+ +G +GV H L + P V Sbjct: 440 LVMQSFCHTAAYPKPVDVKMHRELPQFISSRGGVALRP-GDGVIHSWLNRL--LLPDTVG 496 Query: 119 VGADSHTCTHGAFGAFATGI----GSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTS 174 G DSHT F GI GS +A ATG + +PE++ G++QP +T Sbjct: 497 TGGDSHT-------RFPIGISFPAGSGLVAFGAATGVMPLDMPESVLVRFKGEMQPGITL 549 Query: 175 KDVILSI------IGEVGVDGATYKACQFGG----ETVKKMSIASRMTMTNMAIEMGGKT 224 +D++ SI G + V+ A K G E + + + +++ A E Sbjct: 550 RDLVHSIPLYAIKAGLLTVEKAGKKNVFSGRVLEIEGLPNLKVEQAFELSDAAAERSAAA 609 Query: 225 GIIE-------------------------PDEKTIQYVKEAMKKHGTERPFEVIKGDEDA 259 ++ D +T+Q EA++ +P E++K D DA Sbjct: 610 CSVQLNPEPIAEYLRSNVVLMKNMIANGYEDARTLQRRIEAVEAW-LAKP-ELLKADADA 667 Query: 260 EFAEVYEIE-ADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIGSCTNGRLEDLRMAIKI 318 E+A V EI+ AD EP+ CP++ D+ K EVAG ID+VF+GSC + R A KI Sbjct: 668 EYAAVIEIDLADIKEPIVCCPNDPDDAKFVSEVAGTKIDEVFVGSCMT-NIGHFRAAGKI 726 Query: 319 IEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNPSCSACMGSLYGVLGP 378 +E + VR+ + P ++ + + KEG G + P CS CMG+ + Sbjct: 727 LEGKKDL--PVRLWMAPPTKMDAAELTKEGYYATLGGAGARMEMPGCSLCMGN-QAQIKE 783 Query: 379 GEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 G +STS RNF R G ++L S AA C+ G + Sbjct: 784 GSTAMSTSTRNFPNRLGK-NTNVFLGSAELAAVCSKLGRI 822 Lambda K H 0.318 0.136 0.400 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: 882 Number of extensions: 61 Number of successful extensions: 6 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: 424 Length of database: 863 Length adjustment: 37 Effective length of query: 387 Effective length of database: 826 Effective search space: 319662 Effective search space used: 319662 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 10 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