Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_052669763.1 NITAL_RS17280 aconitate hydratase
Query= curated2:Q8TVF2 (418 letters) >NCBI__GCF_000969705.1:WP_052669763.1 Length = 670 Score = 242 bits (618), Expect = 2e-68 Identities = 153/399 (38%), Positives = 210/399 (52%), Gaps = 9/399 (2%) Query: 21 GDIVVANIDVAMVHDITGPITVQRLEEMGVERVWDPSKIVVLFDHQVPADSVEAAENHKI 80 G + ID + D TG + + LE MG++RV + DH + + + ++H+ Sbjct: 22 GSPIGIRIDQTLTQDATGTLVMLELEAMGLDRVRTEVSAQYV-DHNLVQEDHKNPDDHRF 80 Query: 81 MREFVEEQGIEHFYDVREGVCHQVLPEKGHVRPGDVIVGADSHTCTHGALGAFATGIGST 140 +R E G+ F G+ H V E+ RPG + G+DSHT GA+G A G G Sbjct: 81 LRSACERFGV-WFSRPGNGISHPVHQER-FGRPGATMAGSDSHTPAAGAVGMLAIGSGGL 138 Query: 141 DMAAVFATGKLWFRVPETYRVEITGELPEGVYAKDVVLKVTGEIGADGATYMAIEYHGEV 200 D+A A L R P+ + VE+ GEL + V AKDV+L++ DG IEYHG Sbjct: 139 DVAMAMAGEPLRIRCPQVWGVELVGELHDWVSAKDVILELLRRHDVDGGVGRIIEYHGPG 198 Query: 201 VREMSVSDRMCLCNMAIEMGAKTGMVPPDEKTLEYVKKRAGTEG-RPVEPDPDARYEAEL 259 V +S DR +CNM E+GA T + P DE+ ++ ++ + R + + A Y+ Sbjct: 199 VANLSAMDRHVICNMGAELGATTSVFPADEEVRRFLTRQGRADDFRELVAEDGATYDVTE 258 Query: 260 TLDVSDLEPQVAKPFSPDNVVPVGEVEGIAIDQVFIGSCTNGRYEDLKVAAEVLE--GEE 317 +D+S +EP +A P SP NVVPV EV G I Q +IGS N Y D V A VLE G Sbjct: 259 RIDLSSVEPLIALPTSPGNVVPVREVAGQPIAQAYIGSSANPGYRDFAVVAAVLEATGAT 318 Query: 318 VHDDVRLIVIPASREVYHRTLKDGVLEVLHEAGALICPPNCGPCLGGHMGVLAEGER-CV 376 V DDV L V P SR++ ++DG L L AGA + C C+G MG + + Sbjct: 319 VSDDVSLDVNPTSRQILGELIRDGYLLPLVRAGARLHQAGCNGCIG--MGQAPPTDAISL 376 Query: 377 ATSNRNFPGRMGHRESEVYLASPATAAASAIEGEITDPR 415 T+ RNFPGR G + V+L SP TA ASAI G ITDPR Sbjct: 377 RTTPRNFPGRSGTVDDRVHLCSPETAVASAITGVITDPR 415 Lambda K H 0.317 0.136 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: 720 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 670 Length adjustment: 35 Effective length of query: 383 Effective length of database: 635 Effective search space: 243205 Effective search space used: 243205 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 (21.6 bits) S2: 52 (24.6 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