Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate H281DRAFT_00785 H281DRAFT_00785 2-hydroxy-3-oxopropionate reductase
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__Burk376:H281DRAFT_00785 Length = 302 Score = 158 bits (399), Expect = 2e-43 Identities = 101/276 (36%), Positives = 147/276 (53%), Gaps = 9/276 (3%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M I F+GLG MG MA NLLK GH + V P V + + + + A++ Sbjct: 1 MAKIGFIGLGIMGAHMARNLLKGGHTLFVNGAYP--VPEDLGKSTNVVSDSTAVAQAADI 58 Query: 61 VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120 VI M+P V ++ DDG+ A + L+ID S+I+P + A+ A G+ LDAP Sbjct: 59 VIIMVPDTPDVANVLFADDGVAAGLTAGKLVIDMSSISPLDTQAFAKKINALGVDYLDAP 118 Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180 VSGG GAR TL+ +VGGP + FA+A+P+ E MG+NI GD+GAGQ K+ N +++ + Sbjct: 119 VSGGEVGAREATLTIMVGGPEKAFAQAKPLFELMGKNISLIGDNGAGQTCKVANQIIVAL 178 Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQ 240 + AEAL ++G DP V K GG + + V + + GF+ Sbjct: 179 NIEAVAEALLFASRSGADP---ERVRKALMGGFASSRILE----VHGERMTKRTFNPGFR 231 Query: 241 VRLMNKDLGLALANAQAVQASTPLGALARNLFSLHA 276 + L KDL LAL A+ + + P A A+ LFS+ A Sbjct: 232 IELHQKDLNLALDGARKLGIALPHTASAQQLFSVCA 267 Lambda K H 0.317 0.135 0.395 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: 242 Number of extensions: 12 Number of successful extensions: 3 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: 298 Length of database: 302 Length adjustment: 27 Effective length of query: 271 Effective length of database: 275 Effective search space: 74525 Effective search space used: 74525 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