Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate YP_428592.1 Rru_A3511 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000013085.1:YP_428592.1 Length = 891 Score = 114 bits (286), Expect = 9e-30 Identities = 114/431 (26%), Positives = 181/431 (41%), Gaps = 88/431 (20%) Query: 62 VDH--AAPSPRRELS-----NDQKFIY-EFAKKVGADFN--PPGEGIIHQIMVERYVKPG 111 +DH AA S +R + N +++ + + +K +F PPG GI HQ+ +E Y+ G Sbjct: 133 IDHFGAADSMKRNMDLEFERNGERYAFLRWGQKAFNNFRVVPPGVGICHQVNLE-YLAKG 191 Query: 112 --------------DLAVGADSHTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFR 157 D VG DSHT G+G G+G + A+ +PE Sbjct: 192 VWTGREGDRTLAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPISMLIPEVIG 251 Query: 158 VQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGECAENMTVEERLTIANMAVECG 217 +L GSL +G A D++L ++ L G K +EF G+ +N+ + +R TIANM E G Sbjct: 252 FKLTGSLKEGTTATDLVLTVVEMLRKKGVVGKFVEFFGDGLDNLPLADRATIANMVPEYG 311 Query: 218 AKAGIFESDENTRKFLAELGREGD--------------FREVKADEDAEYEKEIYMDVSS 263 A GIF D T ++L GR+ D +R+ + E + + +D+ + Sbjct: 312 ATCGIFPIDAETLRYLRFTGRDEDSVALVEAYAKAQGMWRQTGSAEPL-FTDTLALDMGT 370 Query: 264 LVPVVSKPHNVDNVAEIS-----------------------EVEGT-------EVNQVYI 293 + P ++ P + +S V GT +V I Sbjct: 371 VEPSLAGPKRPQDRVALSAAAPAFKQALKTLAPEAPADRSIPVAGTDYTLNDGDVVIAAI 430 Query: 294 GTCTNGRLSDLEVAARILKGRKVKEG------VRLIVVPASRRVYLQALDKGLIRVFVEA 347 +CTN + +AA ++ + V+ G V+ + P S+ V GL + Sbjct: 431 TSCTNTSNPSVLMAAGLVAKKAVERGLTSKPWVKTSLAPGSQVVSDYLNKAGLQTYLDQL 490 Query: 348 GGMVLNPGCGPCVGIHQGILADGEV-----------CISTQNRNFKGRMGNPNAEIFLAS 396 G V GC C+G + G LADG + + + NRNF+GR+ +LAS Sbjct: 491 GFNVAGYGCTTCIG-NSGPLADGIIDAVDDNGLVVTAVLSGNRNFEGRISPQVKANYLAS 549 Query: 397 PATAAASAVKG 407 P A A+ G Sbjct: 550 PPLVVAYAIAG 560 Lambda K H 0.318 0.136 0.391 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: 851 Number of extensions: 47 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 416 Length of database: 891 Length adjustment: 37 Effective length of query: 379 Effective length of database: 854 Effective search space: 323666 Effective search space used: 323666 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: 53 (25.0 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