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_010530341.1 ON01_RS07160 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000224785.1:WP_010530341.1 Length = 650 Score = 249 bits (637), Expect = 1e-70 Identities = 143/411 (34%), Positives = 220/411 (53%), Gaps = 5/411 (1%) Query: 3 KTIAEKILSEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTHFFV 62 K I + ++S + K A G +IDQ QD T + + +L +G + + + +V Sbjct: 8 KLIKDHLVSGEMKPGAEIG----LQIDQTLTQDATGTMVMLELEAMGLDYAKTEASAQYV 63 Query: 63 DHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSHTC 122 DH + +D F+ A++ G F+ PG G+ H + ++R PG +G+DSHTC Sbjct: 64 DHNLIQEDNKNPDDHLFLESAAQRFGLHFSRPGNGVSHPVHMQRLAIPGKTLLGSDSHTC 123 Query: 123 TYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGDLG 182 G +G + G G DVA+AI + ++PE V+L G LP V AKDVIL+++ Sbjct: 124 ANGCMGMLAMGAGGIDVAMAITGEPIYIKMPEVMGVKLTGKLPDWVSAKDVILEMLRRHD 183 Query: 183 VDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDF 242 V G K +E++G +++T +R IANM E GA A +F SD ++FL+ RE D+ Sbjct: 184 VKGGVGKIIEYYGPGLDDLTAMDRHVIANMGAELGATATVFPSDNEVKRFLSMQDRENDW 243 Query: 243 REVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNGRLS 302 E+ AD +A Y+ +++S L P+V+KP + NV E+ GT + Q YIG+ N Sbjct: 244 VELTADNNAAYDIHEEINLSELEPLVAKPSSPGNVVPARELAGTPIYQSYIGSSANPGYR 303 Query: 303 DLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVGI 362 D +AA I+K R + GV + P SR++ + + I +++G + GC C+G+ Sbjct: 304 DFAIAAEIVKDRNIATGVSFDINPTSRQMLTNLVKEMHIASLLQSGARLHQAGCNGCIGM 363 Query: 363 HQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413 Q A G + T RNF GR G +FL+SP TAA SA+ G I DPR Sbjct: 364 GQA-PASGRNSLRTTPRNFPGRSGTKEDSVFLSSPETAAVSALTGEITDPR 413 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: 616 Number of extensions: 29 Number of successful extensions: 2 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: 416 Length of database: 650 Length adjustment: 35 Effective length of query: 381 Effective length of database: 615 Effective search space: 234315 Effective search space used: 234315 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 Jul 26 2024. The underlying query database was built on Jul 25 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