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_013517300.1 ALIDE2_RS01650 3-isopropylmalate dehydratase large subunit
Query= curated2:Q9RTI6 (431 letters) >NCBI__GCF_000204645.1:WP_013517300.1 Length = 669 Score = 200 bits (508), Expect = 1e-55 Identities = 157/451 (34%), Positives = 216/451 (47%), Gaps = 44/451 (9%) Query: 4 TIAEKMLAAHSGHDTVVP-----GQLIECATDWVLCHEITTPAALRMLEERGMDRVF--- 55 T+ EK++A H+ P G+ DW HE T A ML + R Sbjct: 212 TLFEKIVARHALATAFTPAHPAAGEGAFVRADWRFIHEYYTGMAAHMLHA-SLGRPLALR 270 Query: 56 DPQKIVAVPDHSVPAMNIKA----------AKMYQKLKSWVQEKGI---------EHFYD 96 DP IV DH+ A +M + +V + G+ E D Sbjct: 271 DPASIVVFEDHTSYVEESPAHVRGGLVPDVRRMVDAQRRFVADHGLRCHRTLTEAEAARD 330 Query: 97 VGRG--GIAHVVLENTGLMKPGQTLVSGDSHTCNAGALGAFATGVGSTDLAGAIYAGKVW 154 G GI+H ++ + PGQ +V DSHT ++GALG A GVG+TD+A A G V Sbjct: 331 DGSNVAGISHAMVTERYAL-PGQLVVGTDSHTPHSGALGCAAFGVGTTDMANAFVTGAVR 389 Query: 155 FKVPETMLIRVTGKTNPGVTPKDIVLEVIKQ--IGADGANYMVMEWVGDYIDQLDMEGRF 212 +P ++ + + G+ PGVT KD+ L ++ I G V E+ G I + + R Sbjct: 390 MTLPASLRVELDGRLAPGVTAKDVALHLLALPFIREGGGVGKVFEFAGAAIAAMSTDERA 449 Query: 213 TLTNMAIEAGGKTGIVAVD-DTTRAYMQQRGVSPEQYTEYQSDPDAKYKVVVEIDAAQVE 271 TLTNM E GG TGIVA D +T R ++RGV + +SDP A Y V+ +D AQV Sbjct: 450 TLTNMTAELGGFTGIVAPDAETVRFLRERRGVDFAPESWMRSDPGAHYAHVIRVDCAQVG 509 Query: 272 PTVAYPHIPSNGRVAG--SDRIRVTHAYVGSCTNGRITDLRDVARIL-----KGRKVAQD 324 P VA P P NG+ + +R+ AY GSCT G+ D +L +G +VA Sbjct: 510 PMVAAPGDPGNGQPLARLARPVRIDIAYGGSCTAGKREDFDHYHAVLRWAADRGLRVAPG 569 Query: 325 VQMIVVPATQAIWKQAAQEGLLEIFVDAGASVSYPSCGACLGM-HSGVLGPDDICISSSN 383 V + + T A+ A G L+ F GA + PSCGAC G P + +S+ N Sbjct: 570 VALYLQFGTTAVRDHCAAAGYLDAFERVGARILQPSCGACGNCGPGGSSDPGQVTVSAIN 629 Query: 384 RNFVGRMGDPSAQIYLASPATVAASAVEGFI 414 RNF GR G S ++LASP TVAASA+ G I Sbjct: 630 RNFPGRGGPGS--VWLASPPTVAASAIAGEI 658 Lambda K H 0.318 0.134 0.398 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: 804 Number of extensions: 43 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: 1 Length of query: 431 Length of database: 669 Length adjustment: 35 Effective length of query: 396 Effective length of database: 634 Effective search space: 251064 Effective search space used: 251064 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: 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