Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate AZOBR_RS24695 AZOBR_RS24695 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__azobra:AZOBR_RS24695 Length = 256 Score = 108 bits (269), Expect = 1e-28 Identities = 88/273 (32%), Positives = 132/273 (48%), Gaps = 42/273 (15%) Query: 7 IAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDL-------------TDNGEKHENLLF 53 +AG+ VTG GIG+A+ + L + V D+ + + H L Sbjct: 11 LAGRVAFVTGGGGGIGRAVCERLAAEGAAVVVADIGAEVAETVAAALRAEGAQAHATAL- 69 Query: 54 QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKI 113 +V RE A+V + E F VD +VN AGI R L PK + DA + + Sbjct: 70 ---NVADRESWGAAVTGLPEAFRGVDIMVNVAGIVRDRSL--PK-------MTDAEWSAV 117 Query: 114 TMINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWA 173 +N +G +L Q RL+ + G I+N+AS A L G+ GQ+ Y+ +KA V TR+ A Sbjct: 118 IDVNLRGTWLGCQTAFRLVGDRGWGRIVNIASTAIL-GTFGQANYSASKAGVVGLTRTAA 176 Query: 174 KELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGK 233 E + G+ V +APG++E T E R + +E+ TP+GR GK Sbjct: 177 LEGARRGILVNAVAPGVVE-----TAIVEGVPDAVRSQWLEK----------TPIGRLGK 221 Query: 234 LSEVADLVAYYISDRSSYITGITTNVAGGKTRG 266 +E+A +VA+ SD ++Y+TG T GG T G Sbjct: 222 PAEIAAVVAFLASDDAAYVTGQTIVADGGATTG 254 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: 187 Number of extensions: 13 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: 266 Length of database: 256 Length adjustment: 25 Effective length of query: 241 Effective length of database: 231 Effective search space: 55671 Effective search space used: 55671 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 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