Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate Ac3H11_2323 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2323 Length = 889 Score = 110 bits (275), Expect = 2e-28 Identities = 107/346 (30%), Positives = 145/346 (41%), Gaps = 49/346 (14%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D VG DSHT ALG A GVG + L R+PE + V L G+ +D +TA Sbjct: 195 DTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASMMRLPEMVGVELTGQRQDGITAT 254 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 D+VL L L +EF G G ++++ R TISNMA E G LF +DE T+ Sbjct: 255 DVVLALTEFLRKAKVVGAYLEFFGEGAAKLTLGDRATISNMAPEYGATAALFCIDEQTLD 314 Query: 234 YERERGIEVEEMYPDE--------------DAKYVREVEMDLSELEPQVAYPFLPSNAKD 279 Y R G E ++ E A Y R + DLS + +A P P Sbjct: 315 YLRLTGREARQVKLVETYAKTAGLWADALAGAVYDRTLRFDLSTVVRNLAGPSNPHARVA 374 Query: 280 VSEAEKERI-----------------KIDQAVIGSCTNGRIEDLRLAAQILK------GR 316 S+ I + A I SCTN +AA +L G Sbjct: 375 TSDLAARGIAGPWALPSPGEGTMPDGAVVIAAITSCTNTSNPRNVIAAALLARNAHRLGL 434 Query: 317 TVSPDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLG--GHMGVLAEGEV 374 T P V+ + PGS+ V + GL+ G + C C G G + + E+ Sbjct: 435 TRKPWVKTSLAPGSRVVELYLKEAGLLTDLEALGFGIVAFACTTCNGMSGALDPAIQQEI 494 Query: 375 --------AISTTNRNFVGRMGHPNSK-VFLASPAVAAASAIKGYI 411 A+ + NRNF GR+ HP +K FLASP + A AI G + Sbjct: 495 IDRDLYATAVLSGNRNFDGRI-HPYAKQAFLASPPLVVAYAIAGTV 539 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: 739 Number of extensions: 39 Number of successful extensions: 4 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: 889 Length adjustment: 37 Effective length of query: 380 Effective length of database: 852 Effective search space: 323760 Effective search space used: 323760 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