Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:B2KBD7 (418 letters) >FitnessBrowser__SynE:Synpcc7942_0903 Length = 861 Score = 125 bits (314), Expect = 5e-33 Identities = 125/455 (27%), Positives = 196/455 (43%), Gaps = 50/455 (10%) Query: 4 TIAEKIISNHSGRR-VKAGEFVIADVDLTAVQDGTGPLTVEELKKAGFTKLANPARTILF 62 T+A+K++ G V+ G + QD TGP+T +E+K+ + F Sbjct: 373 TLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTGPMTRDEMKELACLGFSADLVMQSF 432 Query: 63 IDHAAPSPRKELSNSQVVLRNFAKETGAILSEIGEGVCHQLLAEKYVNPGEILIGADSHT 122 H A P+ + L +F + G + + G+G+ H L + + P + G DSHT Sbjct: 433 C-HTAAYPKPVDIKTHKTLPDFIAQRGGVALKPGDGIIHSWL-NRMLLPDTVGTGGDSHT 490 Query: 123 CTGGALGAFATGMGSTDVAVGMALGKTWLKAPQTFKIEVEGAFKKGVGAKDLILHLIGVI 182 + +F G G VA A+G L P++ + G+ + G+ +D++ + Sbjct: 491 RFPLGI-SFPAGSGL--VAFAAAIGAMPLDMPESVLVRFTGSLQPGITLRDVVNAIPYQA 547 Query: 183 GADGATYKALE-----FHGSTIR-----NMEMADRFTLANMAVEAGAKAGLFFTDEKTRA 232 G + E F G + ++++ F L + E E T A Sbjct: 548 IQQGLLTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDATAERSCAGSTIKLSEDTVA 607 Query: 233 -YLAE----------RGRGD----------------NFKLISADEGADYEKVIKIDASSL 265 YL RG D N +L+SADE A+Y VI+I+ L Sbjct: 608 EYLRSNVALMKNMIARGYEDSRTLARRIRQMEDWLANPQLLSADEDAEYAAVIEINLDEL 667 Query: 266 -EPTVSCPHTVDNTKTVGELKDIKVNQVFIGTCTNGRIEDLRIAAEILKDKKVNPGTRTF 324 EP ++CP+ DN K + E+ ++++FIG+C I R AA++L+ + G R + Sbjct: 668 TEPILACPNDPDNVKKLSEVAGDPIHEIFIGSCMT-NIGHYRAAAKVLEGEG-QVGGRLW 725 Query: 325 ITPASRDVMLAALKEGLIEIFVKAGASVQTPGCGPCVGVHGGILGDGEVCLATQNRNFQG 384 I P +R +EG F AGA ++ PGC C+G + D +T RNF Sbjct: 726 ICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCSLCMGNQARV-ADNTTVFSTSTRNFNN 784 Query: 385 RMGNTKGF-IYLSSPAVAAYSALKGYISDPREILK 418 RMG KG +YL S +AA AL G I E LK Sbjct: 785 RMG--KGAQVYLGSAELAAVCALLGRIPTLEEYLK 817 Lambda K H 0.317 0.135 0.388 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: 767 Number of extensions: 44 Number of successful extensions: 6 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: 418 Length of database: 861 Length adjustment: 37 Effective length of query: 381 Effective length of database: 824 Effective search space: 313944 Effective search space used: 313944 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 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