Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_009489301.1 C683_RS02490 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-13092 (266 letters) >NCBI__GCF_000313915.1:WP_009489301.1 Length = 242 Score = 105 bits (261), Expect = 1e-27 Identities = 79/253 (31%), Positives = 120/253 (47%), Gaps = 24/253 (9%) Query: 10 KTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENLLFQKVDVTSREQVEASVA 69 ++V++TG SSGIGKA + L V D +H N F D+T ++VE Sbjct: 9 QSVVITGCSSGIGKAQAEAFLDKGAMVYGLDCQPCPLEHPNFFFSLCDITKEKEVEK--- 65 Query: 70 AVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQKGLYLVSQAVG 129 V++ VD + N AGI +D P ++ F++I +N +G +L+ A Sbjct: 66 -VLQKIERVDILCNTAGI------LDDFAPSLDTSVE--LFDRIFAVNVRGTFLLCNACL 116 Query: 130 RLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKYGVRVVGIAPG 189 ++A+ KG IINMAS A L G +AY +K A+Y YT+ + + G+R IAPG Sbjct: 117 PKMLAQGKGCIINMASIASLIPGGGGAAYTASKHAIYGYTKQLTYDYARKGIRANAIAPG 176 Query: 190 IMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVADLVAYYISDRS 249 +RT ++ G+ +EI TP GR + E+A + + SD + Sbjct: 177 -----AIRTPMNQKDF-LNGGEIAKEI------AKETPCGRYAEPEEIAQVTLFLASDDA 224 Query: 250 SYITGITTNVAGG 262 YI G V GG Sbjct: 225 RYIYGDIIPVDGG 237 Lambda K H 0.313 0.131 0.361 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: 147 Number of extensions: 7 Number of successful extensions: 3 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: 266 Length of database: 242 Length adjustment: 24 Effective length of query: 242 Effective length of database: 218 Effective search space: 52756 Effective search space used: 52756 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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