Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate Synpcc7942_1573 Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__SynE:Synpcc7942_1573 Length = 266 Score = 137 bits (345), Expect = 2e-37 Identities = 87/266 (32%), Positives = 136/266 (51%), Gaps = 23/266 (8%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRAT----------- 52 +L +++A++TG++ GIG+ +A R EGA V++D + + R Sbjct: 3 KLDNQIALVTGSSQGIGQEIAIRLASEGAS-VVIDYRSHPEGAEETRKQVEAAGAQCHLA 61 Query: 53 --YGDRVLTVSADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRL 110 + V AD+ ++ +VA +++ FG++DIL NNA + P E + +D + Sbjct: 62 KDHAPEGYVVQADLGDVTQVRNLVAESIKHFGKLDILVNNAGMERRAPFWEVTEADYDMV 121 Query: 111 FAVNVKGMFFLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSA 170 VN+KG FF QA+ Q ++E GKIIN+SS + YC +K + T+ Sbjct: 122 LNVNLKGAFFAAQALVQHLLETKRPGKIINISSVHEELPFPNFASYCLSKGGIKMMTRDL 181 Query: 171 ALALAPHKINVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDD 230 A+ L + I +N +APG ++TP + N P E L+G +PL R+G P D Sbjct: 182 AVELGEYGITINNVAPGAIETP-------INTNLLNNPT-ELNALLGN-IPLKRLGKPKD 232 Query: 231 LTGAALFLASADADYITAQTLNVDGG 256 + LFLAS DADYIT T+ DGG Sbjct: 233 IASLVLFLASPDADYITGTTIFADGG 258 Lambda K H 0.321 0.135 0.393 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: 148 Number of extensions: 4 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: 260 Length of database: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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: 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