Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_090442406.1 BLS63_RS08130 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_900100495.1:WP_090442406.1 Length = 247 Score = 135 bits (341), Expect = 6e-37 Identities = 89/254 (35%), Positives = 132/254 (51%), Gaps = 14/254 (5%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGS-STEVQGYA 59 M L+ K+ ++TG + G+G A+A + GA + ER L E G Sbjct: 1 MSLQGKIALVTGASRGIGQAIALELGRQGAVVIGTATSASGAERIAETLKQHGIEGAGLV 60 Query: 60 LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119 LD+ ++E V + A+I + G+ +LVNNAGI RD ++++ KD D++ VIN Sbjct: 61 LDVGNDESVASTLAHIQQHLGQPLILVNNAGITRDNLMLRMKD---------DEWYDVIN 111 Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWAK 178 NL + + M ++ + G I+NI S+ A GN GQ NYAA+KAG+ A+ Sbjct: 112 TNLNSLYRLSKAVLRGMTKA-RFGRIINIGSVVGAMGNAGQVNYAAAKAGLEGFGRALAR 170 Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND- 237 E+ I AVAPG I T+MT + + L +P+GRLG AEEIA V F+ + Sbjct: 171 EVGSRAITVNAVAPGFIDTDMTRELPEAQRDALLTQIPLGRLGQAEEIAKVVAFLASDGA 230 Query: 238 -YVNGRVFEVDGGI 250 YV G V+GG+ Sbjct: 231 AYVTGATIPVNGGM 244 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: 168 Number of extensions: 10 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: 252 Length of database: 247 Length adjustment: 24 Effective length of query: 228 Effective length of database: 223 Effective search space: 50844 Effective search space used: 50844 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 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