Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__Btheta:351600 Length = 747 Score = 196 bits (499), Expect = 2e-54 Identities = 151/452 (33%), Positives = 218/452 (48%), Gaps = 47/452 (10%) Query: 1 MTLAEKIL-----SQKAGRKVEPGE-FLLLEPDIALANDITAPLAIKKFKEYGGKKVKYP 54 +TLAEKIL ++ + + GE ++ PD D TA +A+ +F G +KV P Sbjct: 30 LTLAEKILYAHLFNEGDLKNYKRGEDYVNFRPDRVAMQDATAQMALLQFMNAGKEKVAVP 89 Query: 55 DRVV---LVPDHFTPNKDIKSAMQVK-----MMREFAREQGIEKFFEIGRMGIEHVLLPE 106 V L+ + +DI +A + +R+ + GI F++ G I V+L Sbjct: 90 STVHCDHLIQAYKGAKEDIATATKTNEEVYDFLRDVSSRYGIG-FWKPGAGIIHQVVL-- 146 Query: 107 EGIVKSGDLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVW-FRVPESIKVTLRGK 165 E G ++VG DSHT G LG A GVG D + G W ++P I V L GK Sbjct: 147 ENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGADAVDV-MTGMEWELKMPRIIGVRLTGK 205 Query: 166 FKDLVTAKDLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLF 225 + KD++LKL IL V G IE+ GPG +S G+ TI NM E G T LF Sbjct: 206 LSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGTASLSATGKATICNMGAEVGATTSLF 265 Query: 226 PVDEITIAYERERG--------------IEVEEMYPDEDAKYV-REVEMDLSELEPQVAY 270 P D Y R G + ++ DE KY R +++DLS LEP + Sbjct: 266 PFDGRMATYLRATGRDRIVELAEAVDCELRADQQVTDEPEKYYDRVIDIDLSTLEPYING 325 Query: 271 PFLPSNAKDVSE-AEKERI-----KIDQAVIGSCTNGRIEDLRLAAQI---LKGRTVSPD 321 PF P A +SE AEK + K++ +IGSCTN +DL AA + +K + +S Sbjct: 326 PFTPDAATPISEFAEKVLLNGYPRKMEVGLIGSCTNSSYQDLSRAASLARQVKEKNLSVA 385 Query: 322 VRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLG---GHMGVLAEGEVAIST 378 II PGS+++ A ++G++D F+ G + CGPC+G H +++ Sbjct: 386 SPLIINPGSEQIRATAERDGMMDDFMQIGAVIMANACGPCIGQWKRHTDDPTRKNSIVTS 445 Query: 379 TNRNFVGRM-GHPNSKVFLASPAVAAASAIKG 409 NRNF R G+PN+ F+ASP + A I G Sbjct: 446 FNRNFAKRADGNPNTYAFVASPELTMALTIAG 477 Lambda K H 0.318 0.138 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: 667 Number of extensions: 39 Number of successful extensions: 5 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: 417 Length of database: 747 Length adjustment: 36 Effective length of query: 381 Effective length of database: 711 Effective search space: 270891 Effective search space used: 270891 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 Apr 09 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