Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_013451110.1 CALNI_RS04930 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:O27439 (419 letters) >NCBI__GCF_000183405.1:WP_013451110.1 Length = 850 Score = 109 bits (272), Expect = 4e-28 Identities = 117/455 (25%), Positives = 199/455 (43%), Gaps = 58/455 (12%) Query: 4 TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63 T+++KI+ +A G V G + + D TGP++ + + + R + + + Sbjct: 375 TLAQKIVGKACGLPGVLPGTACEPKMTTVGSQDTTGPMTADELKELACLR-FQADLFMQS 433 Query: 64 FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123 F H + H + FV +G + +GV H L ++P V G DS Sbjct: 434 FCHTAAYPKPADVKMHKTLPSFVIARGGVSLKP-GDGVIHSWLNRL--LLPDTVGTGGDS 490 Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVIL 179 HT F GI GS +A A G + +PE++ +GKL + +DV+ Sbjct: 491 HT-------RFPIGISFPAGSGLVAFAGALGFMPLDMPESVLVKFKGKLNPGITLRDVVN 543 Query: 180 NIIGRVGADGATYMACE-----FAG-----ETVAEMSVSDRMVLSNMAIEMGGKTGIVEP 229 I G +A + F G E + +++V L++ A E ++ Sbjct: 544 AIPYVAIKQGLLTVAKKGKKNIFNGRILEMEGLPDLTVEQAFELTDAAAERSAAAATIKL 603 Query: 230 DEKTL----------------------NYVRRRSG--KPW----RVFKTDPDAPSLSVME 261 E ++ ++RR + W + D +A +V+E Sbjct: 604 SENSVADFLKSNIALMKEMIAEGYQDAETLKRRIAACEKWLEKPELLSRDENAEYAAVIE 663 Query: 262 VDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAILKNRKVS 320 +D+S++ EP +ACP++ D+VK ++EV G +ID+VF+GSC + R A I + K + Sbjct: 664 IDLSEIKEPILACPNDPDDVKLLSEVAGDKIDEVFIGSCMT-NIGHFRAAGKIWEKEKEA 722 Query: 321 DSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGEVSLSTS 380 + R+ + P ++ + + EG I+ + GA P C C+G + V +STS Sbjct: 723 PT-RIWLTPPTKMDAAQLMREGYYSIYSNIGARTEIPGCSLCMGNQARVRSKSTV-ISTS 780 Query: 381 NRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415 RNF R G A VYL SA +AA +A+ G + P Sbjct: 781 TRNFDDRMGD-GARVYLGSAELAAIAALLGKLPTP 814 Lambda K H 0.318 0.135 0.396 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: 798 Number of extensions: 34 Number of successful extensions: 4 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: 419 Length of database: 850 Length adjustment: 37 Effective length of query: 382 Effective length of database: 813 Effective search space: 310566 Effective search space used: 310566 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Jul 25 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