Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_028314768.1 G491_RS0111940 isocitrate dehydrogenase (NADP(+))
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000429905.1:WP_028314768.1 Length = 408 Score = 163 bits (412), Expect = 8e-45 Identities = 126/384 (32%), Positives = 183/384 (47%), Gaps = 63/384 (16%) Query: 7 IEGDGIGKEVVPATIQVLEATGLPFEF------VYAE--AGDEVYKRTGKALPEETIETA 58 IEGDG G ++ AT L+A + + + V+ E AG++ + +TG+ LP+ET++ Sbjct: 27 IEGDGTGPDIWAATQLALDAA-VKYAYKGEKHIVWKEILAGEKAFNQTGEWLPQETLDAI 85 Query: 59 LDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVIV 111 + A + G G V V +R +LD YA +RP + + P+ +D VI Sbjct: 86 QEHVAAIKGPLTTPVGGGIRSVNVAIRQLLDLYACVRPTRYIPPMPSPVREPEKVDMVIF 145 Query: 112 RENTEGLYKGIEAE--------------------IDEGITIATRVITEKACERIFRFAFN 151 RENTE LY GIE E + E I + I+ + +R+ A Sbjct: 146 RENTEDLYAGIEFESGTEEADKLAAFLTREFGSKVPEKAGIGIKPISAQNTKRLVAMAIE 205 Query: 152 LARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEE------------YDD----- 194 A + VT HK N++K T+G F K Y+VA+E +DD Sbjct: 206 YAIANDR----ASVTLMHKGNIMKFTEGAFAKWGYEVAKERFADQTITEQELWDDFDGKR 261 Query: 195 ----IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGD 250 + +D D + ++ +P FDV+ T NL GD +SD A VGGLG+AP ANIGD Sbjct: 262 PEGKVVIKDRIADMLFQQVLLRPDEFDVIATPNLNGDYISDALAAQVGGLGMAPGANIGD 321 Query: 251 EHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTT 310 +FE HG+AP A NP + ILS +ML YLG EAA+ + KAL + ++ T Sbjct: 322 GCAVFEATHGTAPKYANLDKVNPGSLILSGAMMLTYLGWEEAAEALHKALAKTISQKRVT 381 Query: 311 PDLGGNL--NTFEMAEEVAKRVRE 332 DL + T E AK + E Sbjct: 382 YDLARQMPGATEVKCSEFAKALAE 405 Lambda K H 0.318 0.138 0.390 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: 307 Number of extensions: 15 Number of successful extensions: 6 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: 333 Length of database: 408 Length adjustment: 30 Effective length of query: 303 Effective length of database: 378 Effective search space: 114534 Effective search space used: 114534 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: 49 (23.5 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