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 BWI76_RS04675 BWI76_RS04675 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Koxy:BWI76_RS04675 Length = 363 Score = 191 bits (486), Expect = 2e-53 Identities = 129/358 (36%), Positives = 197/358 (55%), Gaps = 26/358 (7%) Query: 4 VCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKAK 58 + V+ GDGIG EV+ +A+K+L + + + G + + G LP+ T+E + Sbjct: 7 IAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQSTVEGCE 66 Query: 59 EADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNF-GIGQLIGKIAD 113 +AD ILFG++ PK P + + ++ LRK F L++N+RP + G+ + AD Sbjct: 67 QADAILFGSVGGPKWEHLPPAEQPERGALLPLRKHFKLFSNLRPAKLYQGLEEFCPLRAD 126 Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRERL-----ENDTAIAERVITRKGSERIIRFAFEYA 168 + A DI+ +RE T +Y G+ + +++ A V R ERI AFE A Sbjct: 127 ---IAANGFDILCVRELTGGIYFGQPKGREGSGQHEKAFDTEVYHRFEIERIAHIAFESA 183 Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227 K R KV+ I KANVL+ + L+ E+ +EI K Y ++E +D+ M LIK P +FD Sbjct: 184 RKR-RHKVTSIDKANVLQ-SSILWREIVSEISKQYPDVELSHMYIDNATMQLIKDPSQFD 241 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMAS 286 V++ +N+FGDILSDE + + G +G+ PSA++ + L+EP GSAPDIAGK IANP+A Sbjct: 242 VLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIAQ 301 Query: 287 ILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL---GGDLKTKDVGDEILNYI 340 ILS+A+L Y + I A+ L T DL + T ++GD I Y+ Sbjct: 302 ILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGAAAVSTDEMGDIIARYV 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: 294 Number of extensions: 15 Number of successful extensions: 7 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: 363 Length adjustment: 29 Effective length of query: 318 Effective length of database: 334 Effective search space: 106212 Effective search space used: 106212 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