Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate WP_057507172.1 ABB28_RS02830 (2Fe-2S)-binding protein
Query= metacyc::MONOMER-18073 (163 letters) >NCBI__GCF_001431535.1:WP_057507172.1 Length = 196 Score = 142 bits (359), Expect = 2e-39 Identities = 71/151 (47%), Positives = 97/151 (64%), Gaps = 3/151 (1%) Query: 12 IKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVKSCTLF 71 +++ +NG + V + L+D LR+ L LTGTK GCD CGACTVL+ G+ + SC Sbjct: 26 LRLTINGEPHTLEVESTVSLLDLLRDRLQLTGTKKGCDHGQCGACTVLVEGRRINSCLTL 85 Query: 72 AVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENPNPSEE 131 AV +GAEITT+EGL+ +LHP+Q+AF ALQCG+CTPG + A L+ E + + Sbjct: 86 AVMQEGAEITTVEGLANGDELHPLQQAFIAKDALQCGYCTPGQLCSAQGLINEGQACTRD 145 Query: 132 EVRDGLHGNICRCTGYQNI---VKAVLDASR 159 +VR+ + GNICRC Y I V AVLD S+ Sbjct: 146 QVRELMSGNICRCGAYPQITDAVMAVLDESQ 176 Lambda K H 0.322 0.138 0.409 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: 4 Number of successful extensions: 1 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: 163 Length of database: 196 Length adjustment: 19 Effective length of query: 144 Effective length of database: 177 Effective search space: 25488 Effective search space used: 25488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 44 (21.6 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