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_037570303.1 BS73_RS06160 aconitate hydratase
Query= curated2:Q9WYC7 (418 letters) >NCBI__GCF_000744815.1:WP_037570303.1 Length = 661 Score = 253 bits (646), Expect = 1e-71 Identities = 151/416 (36%), Positives = 220/416 (52%), Gaps = 6/416 (1%) Query: 4 TLAEKIFSEHV--GRDVKAGEIVLARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLF 61 +LA ++ ++H+ GR + AGE + RVD + QD TG L++ E LG + + + Sbjct: 14 SLAYRLIADHLVEGR-MTAGEEIALRVDQTLTQDATGTLVMQELEALGLDRAQTEVSVQY 72 Query: 62 IDHASPSPRKELSNSQKMMREFGKEMGVKVFDAGDGISHQILAEKYVKPGDLVAGADSHT 121 +DH + + +R G+ G+G+SH + +++ PG +AG+DSHT Sbjct: 73 VDHNLLQADERNAEDHAFLRSAAHRYGLWYSKPGNGVSHPVHMQRFGVPGRSLAGSDSHT 132 Query: 122 CTAGGLGAFGTGMGSTDVAIIFGLGQNWFKVPETIKVVVNGKLQDGVYAKDIILEIARIL 181 C AG LG G+G +VA+ +P + + G+L V AKD+ILE+ R Sbjct: 133 CAAGALGMLAVGVGGLEVALAIAGQPLHLVMPRIRGIRLTGQLPPWVSAKDVILELLRRH 192 Query: 182 GSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGREED 241 G G LE+HG +++++ DR I+NM E+GA A + PSD TR+FL+ GR ED Sbjct: 193 GVKGGVGWILEYHGPGLDHLSAMDRHVIANMGAELGATASVFPSDRVTRDFLRAQGRGED 252 Query: 242 FRELKADPDAVYETEIEIDATTLEPLVSLPHYVDNVRKVSEVEKEKIKIDQVFIGTCTNG 301 F L A PDA Y+ EID +TLEPL++ P +V V EVE E+I Q IG+ N Sbjct: 253 FAMLTAGPDARYDETEEIDLSTLEPLIARPSSPGDVVPVGEVEGEEIA--QSVIGSSANP 310 Query: 302 RLQDLEIALKILEKHGKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGCGPC 361 L+D +A I+ P V L V P SR++ D G + + GA + GC C Sbjct: 311 GLRDFAVAAGIVAGRQTAPGVSLDVNPTSRELLQDLARSGAVLDLIAAGARLHQAGCLGC 370 Query: 362 VGIHMGVLGDGERVLSTQNRNFKGRMGNPNAEIYLASPATAAATAVTGYITDPRRF 417 +G+ G L T RNF GR G ++L SP TAA +A+TG ITDPRR+ Sbjct: 371 IGMGQAPAA-GRNSLRTFPRNFPGRSGTEEDAVWLCSPETAAVSALTGRITDPRRW 425 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: 610 Number of extensions: 23 Number of successful extensions: 3 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: 418 Length of database: 661 Length adjustment: 35 Effective length of query: 383 Effective length of database: 626 Effective search space: 239758 Effective search space used: 239758 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