Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate 8501602 DvMF_2320 6-phosphogluconate dehydrogenase NAD-binding (RefSeq)
Query= metacyc::MONOMER-11664 (295 letters) >FitnessBrowser__Miya:8501602 Length = 287 Score = 141 bits (356), Expect = 2e-38 Identities = 95/290 (32%), Positives = 149/290 (51%), Gaps = 13/290 (4%) Query: 3 IAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELVIT 62 IA +GLG MG MA NL+KAGHQ+ +++ L LG + +PK AAA ++ V+ Sbjct: 4 IAVLGLGAMGRRMAANLLKAGHQVTVWNRTARAAEPLLALGATQAATPKQAAAGADFVLA 63 Query: 63 MLPAAAHVRSVYLN-DDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPVS 121 M+ A +V+L+ + G AG+RPG +D ST+ + + AA +GV + + PVS Sbjct: 64 MVRDDAASATVWLDAETGAFAGMRPGAIAMDSSTLSVDWIKKLGAEAANRGVTLLETPVS 123 Query: 122 GGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGISM 181 G A A L F+VG SA+ +PVL MG + H G++G G + K+ N LLG+ + Sbjct: 124 GSLPQADAAQLIFLVGGSADACRQAEPVLLAMGSAVNHTGDIGAGALTKLATNALLGVQV 183 Query: 182 IGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIE-TAPASRGYTGGFGA 240 ++E + + G D + + GII + WS ++ AP F Sbjct: 184 TAIAELIGMLRRNGADAQKIMGIIAGTA--VWSPYAQRAIGALLSGEAPVM------FPV 235 Query: 241 ELMLKDLGLATEAARQAH-QPVILGAVAQQLYQAMSLRGEGGKDFSAIVE 289 EL+ KD G A EAA P I A A+ +++ +G G + +++V+ Sbjct: 236 ELVEKDFGYALEAAGSPDAAPTI--AAARSVFRRGMDKGLGDANLTSVVK 283 Lambda K H 0.317 0.134 0.386 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: 248 Number of extensions: 17 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: 295 Length of database: 287 Length adjustment: 26 Effective length of query: 269 Effective length of database: 261 Effective search space: 70209 Effective search space used: 70209 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 (21.6 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