Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__MR1:201911 Length = 248 Score = 134 bits (338), Expect = 1e-36 Identities = 86/256 (33%), Positives = 136/256 (53%), Gaps = 21/256 (8%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKL---ALIDVDQDKLERACADLGSSTEVQG 57 + L KV ++TG + G+G A+A +AGA + A + ++ D G G Sbjct: 5 LSLAGKVALVTGASRGIGRAIAETLVEAGAVVIGTATSEKGAAAIQEYLGDKGF-----G 59 Query: 58 YALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSV 117 L++TD + V F I E G +++LVNNAGI RD +L++ KD D++ + Sbjct: 60 LVLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKD---------DEWNDI 110 Query: 118 INVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGW 176 I+ NLT F + M++ + G I+NI S+ GN GQ NY+A+KAG+ + Sbjct: 111 IDTNLTSLFRLSKPVMRTMMKK-RFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSL 169 Query: 177 AKELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN 236 A+E+A I A+APG I T+MT + + + + VP+ RLG A+EIA+ V F+ + Sbjct: 170 AREVASRQITVNAIAPGFIQTDMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASD 229 Query: 237 D--YVNGRVFEVDGGI 250 Y+ G V+GG+ Sbjct: 230 SAAYITGETLHVNGGM 245 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: 7 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: 248 Length adjustment: 24 Effective length of query: 228 Effective length of database: 224 Effective search space: 51072 Effective search space used: 51072 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