Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate 209413 DVU0477 isocitrate dehydrogenase, NADP-dependent
Query= BRENDA::Q4J6C9 (411 letters) >MicrobesOnline__882:209413 Length = 380 Score = 367 bits (943), Expect = e-106 Identities = 177/375 (47%), Positives = 259/375 (69%), Gaps = 6/375 (1%) Query: 29 ILYIEGDGIGPEITNSAIRVVNKAVEKAYKSSREIKWLEVYAGEKANKITGDRFPKETQD 88 + +IEGDGIGPE+ +A V++ AVEK+Y SR I+W E+ AGEKA++ TG+ P+ T D Sbjct: 5 VYWIEGDGIGPEVWKAARPVIDAAVEKSYGDSRSIEWKELLAGEKAHRETGEYLPQSTLD 64 Query: 89 MLLKYRVVLKGPLETPIGKGWKSINVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMI 148 L + +KGPL TP+GKG++S+NV +R LDLYA IRP++Y +G+ SP+K P+ VDM+ Sbjct: 65 TLATAELAIKGPLGTPVGKGFRSLNVTMRQTLDLYACIRPIRYFDGIMSPVKRPDLVDMV 124 Query: 149 IFRENTDDLYRGIEFPYDSEEAKKIRKFLREELKVDIEDDTGIGLKVMSKFKTQRITRLA 208 +FRENT+D+Y GIE+ + EAK++ FLR+EL ++ + +G+K M++ ++R+ R A Sbjct: 125 VFRENTEDVYAGIEYRAGTPEAKRLIAFLRDELGAKVDIEAAVGIKPMTEKGSKRLVRRA 184 Query: 209 LNYALQNSRKKVTVMHKGNVMKYTEGSFREWAYEVALNEYRDKIVTEEEINRGVNSEGKV 268 L +A+ R +T++HKGN+MK+TEG FREW YEVA +E+ D TE E + G++ Sbjct: 185 LRFAIDQKRPNLTLVHKGNIMKFTEGGFREWGYEVARDEFADLTTTETE-----GTAGRL 239 Query: 269 ILNDRIADNMLQQIIIRPDEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDTGGMF 328 ++ DRIAD M Q+++IRP +Y +I N+NGDYISDA A +G +G+ G N+ D+ F Sbjct: 240 VVKDRIADAMFQEVLIRPQQYSVIATSNLNGDYISDALAAQVGGLGLAPGVNMSDSLAFF 299 Query: 329 EAIHGTAPKYAGKNVANPTGIIKSCELMLYFMGWSEAARLIEKAINESIKQKKVTQDIAR 388 EA HGTAP AG++ ANP +I LML MGW+EAA I KA+NE+I ++VT D+A Sbjct: 300 EATHGTAPTIAGQDKANPGSLILCGALMLEHMGWNEAAERIYKAVNEAIASRRVTVDLAT 359 Query: 389 YL-GITPLGTKEYTD 402 + T +GT + D Sbjct: 360 QMENATTVGTVAFGD 374 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: 398 Number of extensions: 12 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: 380 Length adjustment: 31 Effective length of query: 380 Effective length of database: 349 Effective search space: 132620 Effective search space used: 132620 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 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