Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_011386745.1 AMB_RS22255 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P81291 (424 letters) >NCBI__GCF_000009985.1:WP_011386745.1 Length = 861 Score = 127 bits (320), Expect = 1e-33 Identities = 128/460 (27%), Positives = 205/460 (44%), Gaps = 61/460 (13%) Query: 2 GMTIVEKILAKASGKKE---VSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPE 58 G ++ +K++ +A G E + PG + D TGP+T + LK+ ++ + Sbjct: 379 GFSLAQKMVGRACGLPEGKGMRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLG-FSAD 437 Query: 59 KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118 ++ F H + + H + F+ +G +GV H L + P V Sbjct: 438 MVMQSFCHTAAYPKLVDVKTHRELPGFISTRGGVALRP-GDGVIHSWLNRL--LLPDTVG 494 Query: 119 VGADSHTCTHGAFGAFATGI----GSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTS 174 G DSHT F GI GS +A ATG + +PE++ G +QP VT Sbjct: 495 TGGDSHT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTL 547 Query: 175 KDVILSI------IGEVGVDGATYKACQFGG----ETVKKMSIASRMTMTNMAIEMGG-- 222 +D++ +I G + V+ K G E + + + +++ A E Sbjct: 548 RDLVNAIPLYAIRAGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAA 607 Query: 223 ------KTGIIE-----------------PDEKTIQYVKEAMKKHGTERPFEVIKGDEDA 259 K IIE D +T+ +AM+ ++P +++ D DA Sbjct: 608 CSVRLDKAPIIEYMTSNITLMKWMIANGYEDARTLGRRIKAMEAW-IKKP-DLLAPDADA 665 Query: 260 EFAEVYEIE-ADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIGSCTNGRLEDLRMAIKI 318 E+A V EI+ AD EP+ ACP++ D+VK EVAG ID+VFIGSC + R A K+ Sbjct: 666 EYAAVIEIDLADVKEPIVACPNDPDDVKLLSEVAGAKIDEVFIGSCMT-NIGHFRAAGKV 724 Query: 319 IEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTNPSCSACMGSLYGVLGP 378 +E I R+ + P ++ + + +EG K G + P CS CMG+ + Sbjct: 725 LEGKSDI--PTRLWIAPPTKMDAMILNEEGYYSVLGKSGARMEMPGCSLCMGN-QAQIRK 781 Query: 379 GEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 G +STS RNF R G ++ +YL S AA CA+ G++ Sbjct: 782 GSTAMSTSTRNFPNRLG-IDTNVYLGSAELAAVCALMGKI 820 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: 842 Number of extensions: 49 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: 424 Length of database: 861 Length adjustment: 37 Effective length of query: 387 Effective length of database: 824 Effective search space: 318888 Effective search space used: 318888 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