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_012405403.1 BPHY_RS30890 aconitase family protein
Query= curated2:Q8TVF2 (418 letters) >NCBI__GCF_000020045.1:WP_012405403.1 Length = 653 Score = 202 bits (514), Expect = 2e-56 Identities = 146/450 (32%), Positives = 220/450 (48%), Gaps = 45/450 (10%) Query: 3 KTMAEKILSRASGEDAEAGDI------VVANIDVAMVHDI-TGPITVQRLEEMGVER-VW 54 +T+A+KI+ R + A GD D +H+ TG T G ++ Sbjct: 197 RTLAQKIIERHALRTASTGDASTPGQGAFVRADWRFIHEYYTGMATHMLHAAFGKPLPLY 256 Query: 55 DPSKIVVLFDHQVPADSVEAAENHKIM----------REFVEEQGI-EHFY--------- 94 DP I+ DH + E + ++ R FV+E G+ +H Y Sbjct: 257 DPQTILTFEDHLSYSHRSELHIRNGLLPDVRELSAAHRAFVKEYGLTDHGYLSENGSGID 316 Query: 95 DVREGVCHQVLPEKGHVRPGDVIVGADSHTCTHGALGAFATGIGSTDMAAVFATGKLWFR 154 + EG+ H ++ E+ + PG +I G DSHT GALG A G+G+TDMA F TG + Sbjct: 317 EGSEGISHAMMAER-YALPGQLIAGTDSHTPHSGALGCVAFGVGTTDMANAFVTGAVRMT 375 Query: 155 VPETYRVEITGELPEGVYAKDVVLKVTGE--IGADGATYMAIEYHGEVVREMSVSDRMCL 212 VP R+E G + GV AKD+VL++ E I A E+ G + ++S +R L Sbjct: 376 VPLALRIEFNGAIARGVTAKDLVLRLLAEPRIRAGAGVGKIFEFAGSAIAQLSTDERTTL 435 Query: 213 CNMAIEMGAKTGMVPPDEKTLEYVKKRAGTEGRPVEP----DPDARYEAELTLDVSDLEP 268 NM E+G G+V PDE+T+ ++K+R G E +EP DP A+Y + LD + + P Sbjct: 436 TNMTAELGGFAGIVAPDEETVRFLKERRGIE-FTIEPWMHSDPGAQYADVIALDCTQVSP 494 Query: 269 QVAKPFSPDNVVPVGEV-EGIAIDQVFIGSCTNGRYEDLKVAAEVL-----EGEEVHDDV 322 +A P P N + + ++ E ID + GSCT G+ +D EVL G + D + Sbjct: 495 MLAAPGDPGNGIALRDMTERPHIDIAYGGSCTAGKRDDFDHYHEVLAWAAARGLRISDGI 554 Query: 323 RLIVIPASREVYHRTLKDGVLEVLHEAGALICPPNCGPCLGGHMGVLAE-GERCVATSNR 381 +L + + +V + G L+ GA++ P+CG C G E G+ ++ NR Sbjct: 555 KLYLQFGTSDVRDYCIGRGYLDAFERVGAILLQPSCGACANCGPGSSTEQGQVTISAINR 614 Query: 382 NFPGRMGHRESEVYLASPATAAASAIEGEI 411 NFPGR G +V+LASP T ASA+ G I Sbjct: 615 NFPGRSG--PGKVWLASPPTVVASALAGHI 642 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: 642 Number of extensions: 36 Number of successful extensions: 7 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: 653 Length adjustment: 35 Effective length of query: 383 Effective length of database: 618 Effective search space: 236694 Effective search space used: 236694 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 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