Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_011777761.1 MVAN_RS02245 KR domain-containing protein
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000015305.1:WP_011777761.1 Length = 261 Score = 135 bits (339), Expect = 1e-36 Identities = 98/254 (38%), Positives = 131/254 (51%), Gaps = 14/254 (5%) Query: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGS-STEVQGYAL 60 DL V V+TGG G+GL MA A+AGA +A++ +L+ A A L S V Sbjct: 12 DLTGHVAVVTGGGSGIGLGMAEGLARAGATVAILGRSAQRLDSAAATLRSHGNPVLPVVC 71 Query: 61 DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120 D+TDE+ V A I +FG ++ NAG+ G D S +F+ V V Sbjct: 72 DVTDEQAVTDAMARIRSEFGWLDSCFANAGVR--GTFTPTLD------TSLAEFREVTRV 123 Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKE 179 +L G F+ REAA MI +G+ G +V +SSL A G Q YAASKAGV ++ A E Sbjct: 124 DLDGVFVTLREAARQMIGAGRGGSLVGVSSLGAVQGMPRQPAYAASKAGVTSLMDSLAVE 183 Query: 180 LARYNIRSAAVAPGVIATEMTA-AMKPEALE-RLEKLVPVGRLGHAEEIASTVRFIIE-- 235 ARY IR+ + PG ATEMTA M E R+ VPV R G AE++ ++ Sbjct: 184 FARYGIRANTIQPGWFATEMTADGMADERFRARVLPRVPVRRWGAAEDVGGIAVYLASPA 243 Query: 236 NDYVNGRVFEVDGG 249 + Y G V +DGG Sbjct: 244 SAYHTGDVLRLDGG 257 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: 132 Number of extensions: 9 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: 261 Length adjustment: 24 Effective length of query: 228 Effective length of database: 237 Effective search space: 54036 Effective search space used: 54036 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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