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_044409227.1 NA59_RS05490 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:Q1AVC5 (424 letters) >NCBI__GCF_000934765.1:WP_044409227.1 Length = 858 Score = 108 bits (271), Expect = 5e-28 Identities = 121/452 (26%), Positives = 185/452 (40%), Gaps = 55/452 (12%) Query: 3 HTLAEKLLISHSEVDDASPGDIIMVRCDLVMANDVSGPVAFRQMERMGVQRVFDPSKVVM 62 +TLA+K++ V PG V + D +G + +M+ + F V+ Sbjct: 372 YTLAQKMVGQACGVAGVRPGVYCEPHMATVGSQDTTGAMTRDEMKELACLG-FSADFVLQ 430 Query: 63 VSDHFMPAKDARSAALQKRLKSWSDLQGVYYYGQGRGGIEHTVLVEDGWIVPGMVIAGGD 122 H LQ L + +G G G I H+ L + ++P V GGD Sbjct: 431 SFCHTAAYPKPVDIKLQHSLPDFMTSRGGVSLRPGDGVI-HSWL--NRMLLPDTVGTGGD 487 Query: 123 SHT-CTYGALGAFGTGLGSTDIAACLAFGEFWQQVPGTIQVEFTGHKGSFVAGKDLILAV 181 SHT G G+GL +A G +P ++ V F G + +DL+ A+ Sbjct: 488 SHTRFPIGISFPAGSGL----VAFGATLGVMPLNMPESVLVRFKGKMQPGITLRDLVNAI 543 Query: 182 --------IADIGVGGGANA----VLEFVGEGAASLSLDDRLAVANMAVEAGAETGIFPA 229 + + G N VLE EG L ++ +++ + E A + Sbjct: 544 PYQAIQSGLLTVEKKGKKNVFNGRVLEI--EGLPDLKVEQAFELSDASAERSANGCVVKL 601 Query: 230 DEVT----------------------ARYLDRRAD--REWHPE----RSDPDASYVRKVK 261 E + AR L RR D ++W +D DA Y ++ Sbjct: 602 GEASIIEFLKSNIRLIEWMVENGYQDARTLLRRRDEMQKWIDSPVLLEADADAQYAEIIE 661 Query: 262 IDLNSL-EPLVALPHSPGNVVAVSEARGTKIDQVYIGNCSNGTITDLRQTAEILRGNRVH 320 IDL+ + EP+VA P+ P +V +SE G KID+V+IG+C I R ++L + Sbjct: 662 IDLDQIKEPIVACPNDPDDVKLLSEVSGEKIDEVFIGSCMT-NIGHYRAAGKVLENIKGA 720 Query: 321 PDVRAIIVPASQKVYRQAISEGLIDVFVEAGAVVSTPTCGACFGGHMGVLAEGERAITTT 380 + I P ++ RQ I EG F GA P C C G V A+G +T+ Sbjct: 721 VPTKLWIAPPTKMDERQLIEEGYYSTFGRTGARTEMPGCSLCMGNQARV-ADGATVFSTS 779 Query: 381 NRNFKGRMGSPLAEVCLANAYVAAAAAVAGEI 412 RNF R+G+ A V L +A +AA A G+I Sbjct: 780 TRNFPNRLGND-ANVYLGSAELAAVIAAMGKI 810 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: 699 Number of extensions: 32 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: 1 Length of query: 424 Length of database: 858 Length adjustment: 37 Effective length of query: 387 Effective length of database: 821 Effective search space: 317727 Effective search space used: 317727 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