Align Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- (characterized)
to candidate Ac3H11_3259 Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3259 Length = 366 Score = 178 bits (451), Expect = 2e-49 Identities = 119/356 (33%), Positives = 184/356 (51%), Gaps = 28/356 (7%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGEFEIIKGE------AGLECLKKYGNALPEDTIEK 56 ++ +I GDGIGKEV+PE ++++ I E A + +G +P+D + Sbjct: 10 RIALIAGDGIGKEVLPEGLRVVQAAAARFGIALETTTIDWASCDYYAAHGKMMPDDWKAQ 69 Query: 57 AKEADIILFGAITSPK--PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKIADY 114 D I FGA+ P P V + S ++ R+ F Y N+RP+ F G Sbjct: 70 LSGMDAIFFGAVGWPSAVPDHVSLWGS-LLKFRREFDQYINLRPVRLFE-----GVPCPL 123 Query: 115 EFLNAKNIDIVIIRENTEDLYVGR-----ERLENDTAIAERVITRKGSERIIRFAFEYAI 169 +ID ++RENTE Y E + + I E V +R G+ R+++FAF+ A Sbjct: 124 AGRQPGDIDYYVVRENTEGEYTSLGGLMYEGTDREICIQESVYSRHGANRLLKFAFDLAQ 183 Query: 170 KNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFDV 228 +K V+ K+N + I+ + + +++ + Y + D +D + P +FDV Sbjct: 184 SRAKKHVTLATKSNGIAISMPWWDQRADDVAQGYPEVTLDKQHIDILTARFVLQPGRFDV 243 Query: 229 IVTTNMFGDILSDEASALIGGLGLAPSANIGDDK---ALFEPVHGSAPDIAGKGIANPMA 285 + TN+FGDILSD A G +GLAPSAN+ ++ +LFEPVHGSAPDI GK IANP+A Sbjct: 244 VAATNLFGDILSDLGPATTGTIGLAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIA 303 Query: 286 SILSIAMLFDYIGE-----KEKGDLIREAVKYCLINKKVTPDLGGDLKTKDVGDEI 336 I S A++ D++ + + D I A++ + + TPDLGG T VG+ I Sbjct: 304 MIWSGALMLDFLTQGQGAGRAAHDAIVNAIEEVIKSGPRTPDLGGAASTTQVGEAI 359 Lambda K H 0.319 0.140 0.397 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: 325 Number of extensions: 17 Number of successful extensions: 8 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: 347 Length of database: 366 Length adjustment: 29 Effective length of query: 318 Effective length of database: 337 Effective search space: 107166 Effective search space used: 107166 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: 49 (23.5 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