Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate WP_011033474.1 MM_RS07895 aconitate hydratase AcnA
Query= curated2:Q9WYC7 (418 letters) >NCBI__GCF_000007065.1:WP_011033474.1 Length = 935 Score = 115 bits (287), Expect = 7e-30 Identities = 137/519 (26%), Positives = 216/519 (41%), Gaps = 145/519 (27%) Query: 25 LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHA----SPSPRKELSNSQKMM 80 LA + AM + G P IN V A L IDH+ S L ++K Sbjct: 104 LAALRSAMERLGGDPAKINP----------VIPADLVIDHSVQVDSYGTAYSLGENEKKE 153 Query: 81 REFGKEM------GVKVFD------AGDGISHQILAEKYV-------KPGDLVA------ 115 E +E K FD G GI HQ+ E K G+L A Sbjct: 154 FERNRERYTVLRWAQKAFDNFRVVPPGRGIIHQVNLEYLTPLVHLSEKEGELFAFPDTLV 213 Query: 116 GADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQNWFK-VPETIKVVVNGKLQDGVYAKDII 174 G DSHT G+G G G+G + + LGQ ++ VPE + + GKL+ GV A D++ Sbjct: 214 GTDSHTTMINGIGVLGWGVGGIEAEAVM-LGQPYYMPVPEVVGFKLYGKLEPGVTATDLV 272 Query: 175 LEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLK 234 L I ++L G K +EF+G + ++++ DR TISNMA E GA G+ P D++T +++K Sbjct: 273 LTITKMLRKHGVVGKFVEFYGPGLNSLSLPDRATISNMAPEYGATLGIFPPDQETLDYMK 332 Query: 235 KMGREEDFREL-------------KADPDAVYETEIEIDATTLEPLVSLP---------- 271 + GR ++ +L P+ V+ + +E+D T++P ++ P Sbjct: 333 RTGRSDEQVDLVKKYLEAQDLLYSANKPEPVFSSNLELDMGTVKPCLAGPRRPQDQLFLN 392 Query: 272 ----HYVDNVRKVSEVEKE---KIKIDQVFIGTCTNGRLQDLEIALKILEK--------- 315 ++ + +R+ +KE + D ++ G E ++ + Sbjct: 393 EVSENFCETMRQTFIRKKEGGTDLARDPAYLRWIGEGGAPVEETEAQVARETEKVGPVEK 452 Query: 316 -----HG-------------KHPDVRLIVGPASRKVYMDALEKGI-IKKFVE-------- 348 HG +P V + G ++K A+E+G+ +K FV+ Sbjct: 453 DFRVTHGSVVIASITSCTNTSNPSVLIGAGLLAKK----AIERGLKVKPFVKTSLSPGSR 508 Query: 349 -----LGAAVIPP------------GCGPCVGIHMGVLGD------GERVLS-----TQN 380 LGAA + P GC C+G + G L + E+ L+ + N Sbjct: 509 VATEYLGAAGLLPYLEALGFHQVGYGCTTCIG-NSGPLPEHVSKEIEEKDLTVAAVLSGN 567 Query: 381 RNFKGRMGNPNAEIYLASPATAAATAVTGYI-----TDP 414 RNF+GR+ YLASP A A+ G + TDP Sbjct: 568 RNFEGRINPLVKANYLASPPLVVAYAIAGTVNINFETDP 606 Lambda K H 0.318 0.137 0.395 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: 871 Number of extensions: 53 Number of successful extensions: 3 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: 935 Length adjustment: 37 Effective length of query: 381 Effective length of database: 898 Effective search space: 342138 Effective search space used: 342138 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: 54 (25.4 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