Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate WP_028585044.1 G494_RS0113985 isocitrate dehydrogenase (NADP(+))
Query= BRENDA::Q4J6C9 (411 letters) >NCBI__GCF_000429965.1:WP_028585044.1 Length = 405 Score = 396 bits (1017), Expect = e-115 Identities = 190/391 (48%), Positives = 275/391 (70%), Gaps = 4/391 (1%) Query: 19 GKWVVPNKPIILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKIT 78 G V + P I YIEGDGIGP+I +A VV+ A++K Y ++I WLE++AGEKA T Sbjct: 12 GSLNVTDTPTIPYIEGDGIGPDIWAAARNVVDAAIKKTYTGQKKINWLEIFAGEKALDTT 71 Query: 79 GDRFPKETQDMLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESP 138 G+ P+ET D L KY V +KGPL TP+G+G +S+NV +R +LDLYA +RPV+Y +G+ SP Sbjct: 72 GEWLPQETLDALKKYVVGIKGPLTTPVGEGMRSLNVTLRQVLDLYACVRPVRYYQGVVSP 131 Query: 139 LKHPEKVDMIIFRENTDDLYRGIEFPYDSEEAKKIRKFLREELKVDIEDDTGIGLKVMSK 198 +K P VDM+IFRENT+D+Y GIE+ +++A K+ +FLR E+ DI D++GIG+K +S+ Sbjct: 132 VKEPGDVDMVIFRENTEDVYAGIEWQAGTDQANKVIEFLRNEMGADIRDNSGIGIKPISE 191 Query: 199 FKTQRITRLALNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTEEEI 258 F T+R+ R A+ YA+ + R VT++HKGN+MK+TEG+FR W YE+A E+ D ++E+++ Sbjct: 192 FGTKRLVRKAIQYAIDHQRDSVTLVHKGNIMKFTEGAFRNWGYELAAEEFADITISEDDL 251 Query: 259 NRGVNSE---GKVILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGM 315 + N E GK+++ DRIAD M QQI++RP EY ++ PN+NGDY+SDA A +G +G+ Sbjct: 252 WKHHNGELPPGKILIKDRIADAMFQQILLRPREYSVLAMPNLNGDYMSDALAAQVGGLGI 311 Query: 316 LGGANIGDTGGMFEAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAINE 375 GANIGD +FEA HGTAPKYAG + NP ++ S +ML ++GW EAA I+ A+ Sbjct: 312 APGANIGDGVALFEATHGTAPKYAGLDKVNPGSVLLSAVMMLEYLGWQEAADAIKTALET 371 Query: 376 SIKQKKVTQDIARYL-GITPLGTKEYTDTLV 405 +I K VT D+AR + G T L + + ++ Sbjct: 372 TIGDKTVTYDLARLMDGATELSCSAFGEAII 402 Lambda K H 0.317 0.137 0.394 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: 477 Number of extensions: 17 Number of successful extensions: 2 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: 411 Length of database: 405 Length adjustment: 31 Effective length of query: 380 Effective length of database: 374 Effective search space: 142120 Effective search space used: 142120 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 (21.6 bits) S2: 50 (23.9 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