Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate BPHYT_RS23060 BPHYT_RS23060 3-isopropylmalate dehydratase large subunit
Query= curated2:B2KBD7 (418 letters) >FitnessBrowser__BFirm:BPHYT_RS23060 Length = 655 Score = 202 bits (513), Expect = 3e-56 Identities = 150/444 (33%), Positives = 223/444 (50%), Gaps = 38/444 (8%) Query: 2 PQTIAEKIISNH---SGRRVKAGEFVIADVDLTAVQDGTGPLTVEELKKAGFTK---LAN 55 P+T+ EKII H + + G+ V D D + + +A F K L Sbjct: 206 PKTLVEKIIERHLHPASVGAQRGDGVFIAADWRFSHDYFTGMCAHLMHRA-FGKPAPLHA 264 Query: 56 PARTILFIDH------AAPSPRKEL----SNSQVVLRNFAKET-----GAILSEIG-EGV 99 P I F DH + P R L +N +F+++ GA+ G EG+ Sbjct: 265 PDHIIAFQDHLVLASQSIPHVRDGLLPGVANLMEGHTSFSRDYPVRSHGALDGMPGSEGI 324 Query: 100 CHQLLAEKYVNPGEILIGADSHTCTGGALGAFATGMGSTDVAVGMALGKTWLKAPQTFKI 159 CH L+AE+Y PG++ G DSHT GALG A G G+T++A G K P+T +I Sbjct: 325 CHALMAEQYALPGQVACGTDSHTPHSGALGCLAFGAGATEIANSWVTGYVRCKVPETLRI 384 Query: 160 EVEGAFKKGVGAKDLILHLI--GVIGADGATYKALEFHGSTIRNMEMADRFTLANMAVEA 217 E+ G + GV AKD++LHL+ I + GA E+ GS +R M + +R TL NM E Sbjct: 385 EISGQLRDGVTAKDVVLHLLQMDAIRSGGAIGLVFEYGGSAVRAMSIDERATLTNMVAEL 444 Query: 218 GAKAGLFFTDEKTRAYLAERGRGDNFKL---ISADEGADYEKVIKIDASSLEPTVSCPHT 274 G G+ DE+T A+L ER RG +F L + +D GA Y I IDAS+++P ++ P Sbjct: 445 GGFTGIVEPDERTVAFLKER-RGVDFTLENWMKSDAGATYRDTISIDASAIQPMLARPGD 503 Query: 275 VDNTKTVGEL-KDIKVNQVFIGTCTNGRIEDLRIAAEIL-----KDKKVNPGTRTFITPA 328 N +L +D+ ++ + G+CT G+ ED E+L + +V GTR ++ Sbjct: 504 PGNGVPALQLEQDVAIDIAYGGSCTAGKREDFDFYHEVLHWGVEQGLRVPEGTRLYLQFG 563 Query: 329 SRDVMLAALKEGLIEIFVKAGASVQTPGCGPCVGVHGGILGD-GEVCLATQNRNFQGRMG 387 + V + G + +F +AG ++ PGCG C G + EV ++ NRNF GR G Sbjct: 564 TMAVRAYCEERGYLPVFERAGVTLVMPGCGSCANCGPGQSAEANEVTISAINRNFPGRSG 623 Query: 388 NTKGFIYLSSPAVAAYSALKGYIS 411 G ++L+SP A SAL G I+ Sbjct: 624 --PGNVWLASPYTVAASALAGKIT 645 Lambda K H 0.317 0.135 0.388 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: 619 Number of extensions: 32 Number of successful extensions: 8 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: 418 Length of database: 655 Length adjustment: 35 Effective length of query: 383 Effective length of database: 620 Effective search space: 237460 Effective search space used: 237460 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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