Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate Echvi_4068 Echvi_4068 isocitrate dehydrogenase
Query= BRENDA::Q945K7 (374 letters) >FitnessBrowser__Cola:Echvi_4068 Length = 487 Score = 259 bits (662), Expect = 1e-73 Identities = 146/336 (43%), Positives = 214/336 (63%), Gaps = 10/336 (2%) Query: 47 TLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPR-TQSFLTWESLESVRRNKV 105 T+ GDGIGPEI ++ ++ AG IE E +G ++ + S + ++ +S+R K+ Sbjct: 8 TVAYGDGIGPEIMKATLEILEAAGAQIEPEVIEIGEQVYLKGISSGIEPKAWDSLRETKI 67 Query: 106 GLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGY-KTRYDDVDLITIRENTEGE 164 LK P+ TP G G +SLN+T RK L LYANVRPC + Y +T + + D++ +REN E Sbjct: 68 FLKSPITTPQGGGFKSLNVTTRKTLGLYANVRPCKAYSPYIRTHFPETDMVIVRENEEDL 127 Query: 165 YSGLEHQVVRGVVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGLFL 224 Y+G+EH+ V + LK+I+R S ++ YAF YAK + R++V+ + K NIM+ DGLF Sbjct: 128 YAGIEHRQTDDVYQCLKLISRPGSEKIIRYAFEYAKKYNRKKVTCMTKDNIMKLADGLFH 187 Query: 225 KCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLVGGLGL 284 K +VA++YPEI + +ID ++ P +FDV+V NLYGDIISD+ A + G +GL Sbjct: 188 KVFNDVAKEYPEIEADHKIIDIGTALIADKPEMFDVIVTLNLYGDIISDVAAQITGSVGL 247 Query: 285 TPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQAEQIHSAII 344 S N+GED VA+ EA+HGSAPDIAG+N+ANP+ LL +MML H+ E AE++ +A + Sbjct: 248 GGSSNVGED-VAMFEAIHGSAPDIAGQNIANPSGLLNGAIMMLVHIGQPEVAEKVSNAWM 306 Query: 345 NTIAEGKYRTADL---GGSST---TTEFTKAICDHL 374 T+ +G T D+ G SS T EF +A+ D L Sbjct: 307 KTLEDG-IHTGDIYQEGVSSQLVGTKEFAQAVIDRL 341 Lambda K H 0.318 0.134 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: 415 Number of extensions: 19 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: 374 Length of database: 487 Length adjustment: 32 Effective length of query: 342 Effective length of database: 455 Effective search space: 155610 Effective search space used: 155610 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: 51 (24.3 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