Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 208498 DVU2985 3-isopropylmalate dehydrogenase
Query= BRENDA::Q58991 (347 letters) >MicrobesOnline__882:208498 Length = 357 Score = 188 bits (478), Expect = 2e-52 Identities = 122/338 (36%), Positives = 187/338 (55%), Gaps = 20/338 (5%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEK 56 M +C++ GDGIG E++ + K+L+ + G + G+ LP+ T+E Sbjct: 3 MNICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEA 62 Query: 57 AKEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIAD 113 + +D +L GA+ PK ++ + K P ++ +RK L+AN+RP F +L G Sbjct: 63 CRTSDAVLLGAVGGPKWDDLPSEKRPEKGLLGIRKALGLFANLRPAALFP--ELAGACLL 120 Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRE-----RLENDTAIAERVITRKGSERIIRFAFEYA 168 + A +D+V++RE T D+Y G+ R T + RI R AF+ A Sbjct: 121 RADIAAAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNTMIYDEDEVRRIARVAFDTA 180 Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227 + +++V + KANVL T L+ EV E+ + Y ++E VD+ AM L++ P +FD Sbjct: 181 -RARKRRVCSVDKANVLA-TSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFD 238 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGD-DKALFEPVHGSAPDIAGKGIANPMAS 286 VIVT N+FGDILSDEA+ + G +G+ PSA++G ALFEP+HGSAPDIAG+ ANP+A+ Sbjct: 239 VIVTGNLFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIAT 298 Query: 287 ILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL 323 ILS+ M+ G + D I AV+ L T D+ Sbjct: 299 ILSVGMMLRLGFGLAAEADAIDAAVRRVLAEGYRTGDI 336 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: 317 Number of extensions: 24 Number of successful extensions: 6 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: 357 Length adjustment: 29 Effective length of query: 318 Effective length of database: 328 Effective search space: 104304 Effective search space used: 104304 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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