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_004511698.1 GMET_RS13850 aconitate hydratase
Query= curated2:Q9WYC7 (418 letters) >NCBI__GCF_000012925.1:WP_004511698.1 Length = 648 Score = 267 bits (682), Expect = 8e-76 Identities = 153/417 (36%), Positives = 226/417 (54%), Gaps = 4/417 (0%) Query: 1 MGKTLAEKIFSEHVGR-DVKAGEIVLARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAF 59 MGK LA KI H+ + ++K G + ++D A+ QD TG + + EF +G VKV A Sbjct: 1 MGKNLATKILEAHLAKGELKPGTEIALKIDHALLQDATGTMAMLEFIAMGVDRVKVELAA 60 Query: 60 LFIDHASPSPRKELSNSQKMMREFGKEMGVKVFDAGDGISHQILAEKYVKPGDLVAGADS 119 +IDH ++ + + G+ V G+G+SHQ+ E++ PG + GADS Sbjct: 61 QYIDHNLLQTDNRNADDHIFLMTAAQRFGIHVSKPGNGVSHQVHLERFGVPGKTMLGADS 120 Query: 120 HTCTAGGLGAFGTGMGSTDVAIIFGLGQNWFKVPETIKVVVNGKLQDGVYAKDIILEIAR 179 HT +A GL G G DV++ P+ V + G+LQ V AKD+ILE+ R Sbjct: 121 HTTSAAGLSMIAIGAGGLDVSLAMAGHPFHLPCPKIWGVKLTGELQPWVSAKDVILEMLR 180 Query: 180 ILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGRE 239 G K +E++G + ++ DR I NM E+GA + PSD +TREFL+ GR Sbjct: 181 RHTVKGGVGKIIEYYGPGVATLSATDRAIIGNMGAELGATTSVFPSDHRTREFLEAQGRG 240 Query: 240 EDFRELKADPDAVYETEIEIDATTLEPLVSLPHYVDNVRKVSEVEKEKIKIDQVFIGTCT 299 + ++EL ADPDA Y+ EID T+EPL++ P DNV +V+++ E +K+DQV +G+ Sbjct: 241 QLWQELAADPDATYDEYEEIDLATVEPLIARPSSPDNVVRVADI--EGLKVDQVLVGSSA 298 Query: 300 NGRLQDLEIALKILEKHGKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGCG 359 N +DL +IL+ P + V P SR+V + ++G I + GA + PGC Sbjct: 299 NSAFRDLMTVCRILDGRRIAPHLSFNVNPGSRQVLENVADQGGIMMLLLAGAQIHQPGCL 358 Query: 360 PCVGIHMGVLGDGERVLSTQNRNFKGRMGNPNAEIYLASPATAAATAVTGYITDPRR 416 C+G+ G + L T RNF GR G N +YL SP TAAA + G +TDPR+ Sbjct: 359 GCIGMGQAP-GTNQVSLRTFPRNFPGRSGTKNDLVYLCSPETAAAAGLFGVVTDPRK 414 Lambda K H 0.318 0.137 0.395 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: 635 Number of extensions: 33 Number of successful extensions: 4 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: 648 Length adjustment: 35 Effective length of query: 383 Effective length of database: 613 Effective search space: 234779 Effective search space used: 234779 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