Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_012977547.1 AZL_RS26840 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:Q1AVC5 (424 letters) >NCBI__GCF_000010725.1:WP_012977547.1 Length = 863 Score = 97.4 bits (241), Expect = 1e-24 Identities = 99/343 (28%), Positives = 149/343 (43%), Gaps = 52/343 (15%) Query: 112 IVPGMVIAGGDSHT-CTYGALGAFGTGLGSTDIAACLAFGEFWQQVPGTIQVEFTGHKGS 170 ++P V GGDSHT G G+GL +A A G +P ++ V F G Sbjct: 488 LLPDTVGTGGDSHTRFPIGISFPAGSGL----VAFAAATGVMPLDMPESVLVRFKGTMQP 543 Query: 171 FVAGKDLILAV--------IADIGVGGGANA----VLEFVGEGAASLSLDDRLAVANMAV 218 V +DL+ A+ + + G N +LE EG L ++ + + + Sbjct: 544 GVTLRDLVNAIPLYAIKAGLLTVEKKGKKNIFSGRILEI--EGLPDLKVEQAFELTDASA 601 Query: 219 EAGAE--TGIFPADEVT--------------------ARYLDRR--ADREWHPE----RS 250 E A T + + + AR L+RR A W + + Sbjct: 602 ERSAAGCTVLLNKEPIIEYMTSNITLMKWMIANGYADARTLERRIKAMEAWIADPQLLKP 661 Query: 251 DPDASYVRKVKIDLNSL-EPLVALPHSPGNVVAVSEARGTKIDQVYIGNCSNGTITDLRQ 309 D DA Y ++IDL + EP++A P+ P +V +SE G KID+V+IG+C I R Sbjct: 662 DVDAEYAAVIEIDLADIKEPILACPNDPDDVKTLSEVAGDKIDEVFIGSCMT-NIGHFRA 720 Query: 310 TAEILRGNRVHPDVRAIIVPASQKVYRQAISEGLIDVFVEAGAVVSTPTCGACFGGHMGV 369 +IL G P R I P ++ EG +AGA + P C C G V Sbjct: 721 AGKILNGKSDIP-TRLWIAPPTKMDAMMLTEEGYYATLGKAGARMEMPGCSLCMGNQAQV 779 Query: 370 LAEGERAITTTNRNFKGRMGSPLAEVCLANAYVAAAAAVAGEI 412 +G A++T+ RNF R+G V L++A +AA AA+ G+I Sbjct: 780 -RKGSTAVSTSTRNFPNRLGID-TRVYLSSAELAAVAALLGKI 820 Lambda K H 0.319 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: 735 Number of extensions: 30 Number of successful extensions: 5 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 ( 7.4 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