Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate AO356_27315 AO356_27315 short-chain dehydrogenase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27315 Length = 249 Score = 126 bits (316), Expect = 5e-34 Identities = 85/258 (32%), Positives = 144/258 (55%), Gaps = 20/258 (7%) Query: 1 MDLKDKVVVITGGAG--GLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGY 58 M L+ KV +ITG A G+G A A FA+ GA + ++D+D+ A A LG G Sbjct: 1 MLLQGKVAIITGAASERGIGRATAVTFARHGAHVVILDLDESAARDAAATLGEGH--LGL 58 Query: 59 ALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118 A ++ DE V A A ++E +G+I++L+NNAGI + +K D + D + V+ Sbjct: 59 AANVADEMQVKAAVAKVVERYGRIDILINNAGITQP---IKTLDIRPGD------YDKVL 109 Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAK---AGNVGQSNYAASKAGVAAMSVG 175 +V+L GT L +A ++ + +G IV +SS++ G G +Y+A+KAGV + Sbjct: 110 DVSLRGTLLMS-QAVIPVMRTQASGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLGKA 168 Query: 176 WAKELARYNIRSAAVAPGVIATEMTAA-MKPEALERLEKLVPVGRLGHAEEIASTVRFII 234 A+E NIR ++ PG+I T++T M+ + + + +P+GRLG A+++A+ F+ Sbjct: 169 MAREFGADNIRVNSITPGLIHTDITGGLMQDDRRHAIIESIPLGRLGAAQDVANAALFLA 228 Query: 235 E--NDYVNGRVFEVDGGI 250 + Y+ G +V+GG+ Sbjct: 229 SDLSSYLTGITLDVNGGM 246 Lambda K H 0.317 0.134 0.369 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: 134 Number of extensions: 7 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: 252 Length of database: 249 Length adjustment: 24 Effective length of query: 228 Effective length of database: 225 Effective search space: 51300 Effective search space used: 51300 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: 46 (22.3 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