Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 5211055 Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q58991 (347 letters) >FitnessBrowser__PV4:5211055 Length = 364 Score = 182 bits (462), Expect = 1e-50 Identities = 125/364 (34%), Positives = 201/364 (55%), Gaps = 29/364 (7%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 +V V+ GDGIG EV+ EA K+L + E E + + G + +G LPE T++ Sbjct: 4 QVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTLKGC 63 Query: 58 KEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPIN-NFGIGQLIGKIA 112 +EAD ILFG++ PK P + + ++ LR F L+ N+RP + G+ + + Sbjct: 64 EEADAILFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHVGLEHMSPLRS 123 Query: 113 DYEFLNAKNIDIVIIRENTEDLYVGRERL-----ENDTAIAERVITRKGSERIIRFAFEY 167 D ++A+ D++ +RE T +Y G+ + E + A +R+ RI + AFE Sbjct: 124 D---ISAQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEAFDTMRYSRREVRRIAKIAFE- 179 Query: 168 AIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKF 226 A + RKKV+ + KANVL + L+ EV E+ K + ++ + +D+ M L++ P F Sbjct: 180 AARGRRKKVTSVDKANVLACSV-LWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFDF 238 Query: 227 DVIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMA 285 DV++ +N+FGDI+SDE + L G +GL S ++ D L+EP GSAPDIAG+GIANP+A Sbjct: 239 DVMLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIA 298 Query: 286 SILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL------GGDLKTKDVGDEILN 338 ILS A+L + + E+ I +AV L + +T +L T+++GD I Sbjct: 299 QILSAALLLRHSLKEEAAAKAIEDAVAKALSDGYLTGELLPADQRDKAKSTREMGDYIAQ 358 Query: 339 YIRK 342 +R+ Sbjct: 359 AVRE 362 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: 307 Number of extensions: 15 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: 364 Length adjustment: 29 Effective length of query: 318 Effective length of database: 335 Effective search space: 106530 Effective search space used: 106530 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