Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AZOBR_RS29190 AZOBR_RS29190 hydroxyacid dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_05985 (294 letters) >FitnessBrowser__azobra:AZOBR_RS29190 Length = 300 Score = 162 bits (411), Expect = 7e-45 Identities = 110/288 (38%), Positives = 146/288 (50%), Gaps = 8/288 (2%) Query: 3 IAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAELAQLGGTISATAREAAQGAELVIT 62 IAFIGLG MG PMA NL++ S+ DL++ L +L LG + A + A +VIT Sbjct: 5 IAFIGLGAMGLPMASNLVRKNFSVIGFDLDQGKLDKLVALGARPAGDVTAAVRDATVVIT 64 Query: 63 MLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPVSG 122 MLPA VR V LG GVLAG+ G +D ST+DPQT VAAA ++G+A DAPV Sbjct: 65 MLPAPPQVREVILGGAGVLAGLRPGSLVIDMSTVDPQTTDTVAAACLEKGIAFVDAPVGR 124 Query: 123 GTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAISMV 182 A G FMVGA+ FA +P+L MG + CG G G KI NN L I Sbjct: 125 LVSHAERGESLFMVGASDAGFARAEPMLNAMGTTVHRCGPEGAGTRMKIVNNYLAVIGAQ 184 Query: 183 GVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIV-ETAPASRGYTGGFGAE 241 +EA+ LG LG+ V+ + +T ++ + +TAP GF + Sbjct: 185 LTAEAILLGTKLGLPVDVMKAVSGGTTATNGQFQINFATKVLKGDTAP-------GFTID 237 Query: 242 LMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAIIN 289 L KDL LA AA Q + +G A A +DFSA+++ Sbjct: 238 LAHKDLMLALTAAAQQRLGLPVGLAAAGALGAARGGAYAQRDFSALLD 285 Lambda K H 0.317 0.132 0.382 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: 225 Number of extensions: 13 Number of successful extensions: 2 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: 294 Length of database: 300 Length adjustment: 26 Effective length of query: 268 Effective length of database: 274 Effective search space: 73432 Effective search space used: 73432 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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