Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= curated2:O27439 (419 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 Length = 866 Score = 105 bits (262), Expect = 5e-27 Identities = 110/458 (24%), Positives = 197/458 (43%), Gaps = 69/458 (15%) Query: 4 TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63 T+++K++ +A G V G + + D TGP++ + + + + + ++ Sbjct: 383 TLAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLA-CLGFSTDLVMQS 441 Query: 64 FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123 F H H + DF+ +G + +G+ H L ++P V G DS Sbjct: 442 FCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRP-GDGIIHSWLNRM--LLPDTVGTGGDS 498 Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVI- 178 HT F GI GS +A ATG + +PE++ +G+L+ V +D++ Sbjct: 499 HT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGELQPGVTLRDLVH 551 Query: 179 ----------LNIIGRVGADGATYMACEFAG-----ETVAEMSVSDRMVLSNMAIEMGG- 222 L + + G A F+G E + +++V LS+ + E Sbjct: 552 AIPYYAIQAGLLTVEKKGKKNA------FSGRILEIEGLPKLTVEQAFELSDASAERSAA 605 Query: 223 -------KTGIVEPDEKTLNYVRRRSGKPW--------------------RVFKTDPDAP 255 K I E + + +R G+ + + + D DA Sbjct: 606 GCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELLEADKDAE 665 Query: 256 SLSVMEVDVSDLEPQVAC-PHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAIL 314 V+E+D++D++ V C P++ D+ + ++ V G +ID+VF+GSC + R A +L Sbjct: 666 YAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHFRAAGKLL 724 Query: 315 KNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGE 374 + K R+ + P ++ + +EG I+ AGA + P C C+G V P Sbjct: 725 EQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQ-ARVEPNS 783 Query: 375 VSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSI 412 +STS RNF R G A VYL+SA +A+ +++ G + Sbjct: 784 TVVSTSTRNFPNRLGD-GANVYLASAELASVASILGRL 820 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: 817 Number of extensions: 42 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: 419 Length of database: 866 Length adjustment: 37 Effective length of query: 382 Effective length of database: 829 Effective search space: 316678 Effective search space used: 316678 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