Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF2930 PS417_14990 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:B2V844 (431 letters) >FitnessBrowser__WCS417:GFF2930 Length = 869 Score = 101 bits (251), Expect = 1e-25 Identities = 127/474 (26%), Positives = 195/474 (41%), Gaps = 75/474 (15%) Query: 2 GMTITEKIIAAHAGRDY---VEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPN 58 G T+ +K++ G V PG K+ + D T P+ +L+ D Sbjct: 381 GFTLAQKMVGKACGLPEGKGVRPGTYCEPKMTTVGSQDTTGPMTRDELK----DLACLGF 436 Query: 59 KIALVMDHF-----FP-PKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGF 112 LVM F +P P D+ + + DF G + G G++H+ L Sbjct: 437 STDLVMQSFCHTAAYPKPIDVTTHHTLP---DFIMTRGGVSLRPGD--GIIHSWLNR--M 489 Query: 113 VVPGDLVIGADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKW 172 ++P + G DSHT GI S GS +A+ ATG L +PES+ F K + Sbjct: 490 LLPDTVGTGGDSHTRFPMGI---SFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPG 546 Query: 173 VGGKDFV-----------LTVIGKIGVDGALY-KAMEYQGEAIRALDIDNRLTIANMAIE 220 + +D V L + K G A + +E +G L+ L+ A+ Sbjct: 547 ITLRDLVHAIPYYAIQSGLLTVEKKGKKNAFSGRILEIEGLNDLTLEQAFELSDASAERS 606 Query: 221 AGG------KSGIIE-----------------PDEKTVD--------WVRKRTNREFKLY 249 A G K I E D +T++ WV+ +L Sbjct: 607 AAGCTIKLSKESITEYLNSNITLLRWMIGEGYGDPRTLERRAQAMEAWVKNP-----ELM 661 Query: 250 KSDPDAKYCCEYEFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDL 308 ++D DA+Y E D ++I EP++ P+ P + + +S VAG ID+VFIGSC + Sbjct: 662 EADADAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHF 720 Query: 309 RIAAAILKSKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHM 368 R A +L+ K R + P + Q EG I AG + C C+G Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780 Query: 369 GILAEGEVCLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKY 422 + V +STS RNF R+G + VYL+S +AA ++ LGR+ +E Y Sbjct: 781 RVEPNSTV-VSTSTRNFPNRLG-DGANVYLASAELAAVASTLGRLPTVEEYMGY 832 Lambda K H 0.319 0.137 0.407 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: 852 Number of extensions: 41 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: 431 Length of database: 869 Length adjustment: 37 Effective length of query: 394 Effective length of database: 832 Effective search space: 327808 Effective search space used: 327808 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 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