Align Isocitrate--homoisocitrate dehydrogenase; HICDH; Beta-decarboxylating dehydrogenase; EC 1.1.1.286 (characterized)
to candidate Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase
Query= SwissProt::O59394 (345 letters) >FitnessBrowser__Cola:Echvi_2062 Length = 353 Score = 184 bits (467), Expect = 3e-51 Identities = 123/351 (35%), Positives = 196/351 (55%), Gaps = 33/351 (9%) Query: 4 VAVIKGDGIGPEVIDAAIRVVKSVTDK----IKFYEFEGGLSVFKKYGVPIREEDLEEIR 59 +A++ GDGIGPEVI+ ++VVK+V K I F E G + G P +E E Sbjct: 3 IALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDATGNPYPDETHEICL 62 Query: 60 KMDAILFGATTTP-FDVP-----RYKSLIITLRKELDLYANLR-------IIPNFKLRKE 106 + DA+LFGA P +D R + ++ +RK+L L++N+R +I L+KE Sbjct: 63 QADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRPTFTFPSLIHKSPLKKE 122 Query: 107 ------IIIVRENSEGLYSGEGA---YDSNKVVDFRIITRKGAERIAKFAVKLAKDRSTF 157 ++ +RE + G+Y GE K D + T++ R+A+ + A+ R Sbjct: 123 RIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFEFAQKRRKL 182 Query: 158 LTFVHKANILESDRFFRKIVLDIARK-EDVKVREEIVDSFTIKLVKDPWNLGIILSENMF 216 LT V KAN+L + R +R+ V ++ + DVKV E VD+ ++L++ P ++++EN+F Sbjct: 183 LTCVDKANVLATSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKAYDVLITENLF 242 Query: 217 GDILSDLATIHAGSIGIVPSGNYGEDIALFEPIHGSAPDIAGKGIANPIGAILSAAMMLD 276 GDIL+D A++ +GS+G++PS + G D+ LFEPIHGS P AGK IANP+ +LSAAMM + Sbjct: 243 GDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLATVLSAAMMFE 302 Query: 277 Y---LGLDGSIIWKAVGRYVRRGNLTPDMEGR---ATTLEVTNGIISEIYR 321 Y L + I V + G +T D+ + T EV + + ++I + Sbjct: 303 YAFDLKDEAKAISDVVNLSLAEGVVTEDIAEESKPSKTSEVGDWLAAQILK 353 Lambda K H 0.321 0.142 0.403 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: 313 Number of extensions: 17 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: 345 Length of database: 353 Length adjustment: 29 Effective length of query: 316 Effective length of database: 324 Effective search space: 102384 Effective search space used: 102384 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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