Align 3-isopropylmalate dehydrogenase; EC 1.1.1.85; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH (uncharacterized)
to candidate BWI76_RS11330 BWI76_RS11330 isocitrate dehydrogenase (NADP(+))
Query= curated2:B0RIP4 (355 letters) >FitnessBrowser__Koxy:BWI76_RS11330 Length = 416 Score = 118 bits (295), Expect = 3e-31 Identities = 112/401 (27%), Positives = 164/401 (40%), Gaps = 63/401 (15%) Query: 1 MPRTISLAVVPGDGIGPEVVHEALRVLREAVP----ADVSLDTTQYPFGAGHFLETGQI- 55 +P + + GDGIG +V L+V+ AV + + + G GQ Sbjct: 23 VPNNPIIPFIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEVYTGEKSTQVYGQDV 82 Query: 56 -LTDSDLAALAQHDAILLGAVGGDPRDARLAGGIIERGLLLKLRFAFDHYINLRPTALLP 114 L L + ++ + G P + GGI R L + LR D Y+ LRP Sbjct: 83 WLPAETLDLIREYRVAIKG-----PLTTPVGGGI--RSLNVALRQELDLYVCLRPVRYYQ 135 Query: 115 GVASPLAAPGQVDFVVVREGTEGPYAG-------------------NGGVLRRGTEHEIA 155 G SP+ P D V+ RE +E YAG GV + Sbjct: 136 GTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSAEADKVIKFLRDEMGVKKIRFPEHCG 195 Query: 156 TEVSVNTAHGVERTVRFAFELAEKRDRKRVTLVHKTNVLTFAGSLWQRTVDRVAAEH--- 212 + + G +R VR A E A DR +TLVHK N++ F ++ ++A E Sbjct: 196 IGIKPCSEEGTKRLVRAAIEYAITNDRDSLTLVHKGNIMKFTEGAFKDWGYQLAREEFGG 255 Query: 213 -----------------PDVTVDYLHVDATMIFLVTDPSRFDVIVSDNLFGDIITDLAAA 255 ++ V + DA + ++ P+ +DVI NL GD I+D AA Sbjct: 256 ELIDGGPWLKIKNPNTGKEIVVKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAA 315 Query: 256 ISGGIGLAASGNVNPTGAFPSMFEPVHGSAPDIAGQQKADPTAAILSVALLLDHLGLSEA 315 GGIG+A N+ A +FE HG+AP AGQ K +P + ILS ++L H+ EA Sbjct: 316 QVGGIGIAPGANIGDECA---LFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMQWFEA 372 Query: 316 AARVSAAVSDDLAA--------RATGDAAPRSTAEVGDAIL 348 A + +AA R A +E GDAI+ Sbjct: 373 ADLIVKGTEGAIAAKTVTYDFERLMEGAKLLKCSEFGDAII 413 Lambda K H 0.319 0.136 0.389 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: 292 Number of extensions: 20 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: 355 Length of database: 416 Length adjustment: 30 Effective length of query: 325 Effective length of database: 386 Effective search space: 125450 Effective search space used: 125450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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