Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Phaeo:GFF3147 Length = 253 Score = 121 bits (303), Expect = 2e-32 Identities = 83/271 (30%), Positives = 136/271 (50%), Gaps = 32/271 (11%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDL---------TDNGEKH--ENLLF 53 + +AGK IVTG +SG G IV + L+ +V D+ +D E + + + Sbjct: 1 MRLAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPDRAIA 60 Query: 54 QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGIN-IPRLLVDPKDPHGQYELDDATFEK 112 Q VDV+ R V+ A + HFG +D +VNNAG++ +P L D + + F++ Sbjct: 61 QTVDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLED---------VSEEDFDR 111 Query: 113 ITMINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSW 172 + +N K +YL ++A+ + +++ G I+N+AS AG+ + Y +K + + TR+ Sbjct: 112 VVAVNMKSVYLTARALVPHMKSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTM 171 Query: 173 AKELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSG 232 A EL GVRV I P E L+T G+ E+RA + S T P+GR Sbjct: 172 AVELAPAGVRVNAINPVAGETPLLKTF---------MGEDTPEVRAKFLS--TIPIGRFS 220 Query: 233 KLSEVADLVAYYISDRSSYITGITTNVAGGK 263 ++ + Y SD +S +TG+ V GG+ Sbjct: 221 TPEDMGNAACYLCSDEASMVTGVALEVDGGR 251 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: 150 Number of extensions: 5 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: 253 Length adjustment: 24 Effective length of query: 242 Effective length of database: 229 Effective search space: 55418 Effective search space used: 55418 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