Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__PV4:5210421 Length = 255 Score = 103 bits (258), Expect = 3e-27 Identities = 83/273 (30%), Positives = 125/273 (45%), Gaps = 40/273 (14%) Query: 6 NIAGKTVIVTGASSGIGKAIVDELLSLKVKV------------ANFDLTDNGEKHENLLF 53 +++G+ +VTGAS GIG AI + L + V + DNG E + Sbjct: 8 DLSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAMAC 67 Query: 54 QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDA--TFE 111 D+ E ++A+ + G +D +VNNA N P+ + LD F Sbjct: 68 HVGDL---EAIQATFEQIQAKHGRLDILVNNAATN----------PYFGHILDTDLNAFN 114 Query: 112 KITMINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRS 171 K +N +G + +S GR++ + GVI+N AS L+ E Q Y+ +KAAV S T++ Sbjct: 115 KTMEVNLRGYFFMSVTAGRMMREQGHGVILNTASVNALQPGEMQGIYSISKAAVVSMTKA 174 Query: 172 WAKELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRS 231 +AKE G+R + PG + L + K +++ A P+GR Sbjct: 175 FAKECAPLGIRCNALLPGFTKTQFAGAL-------FNNDKIYQQLIA------RIPMGRH 221 Query: 232 GKLSEVADLVAYYISDRSSYITGITTNVAGGKT 264 SE+A V Y +SD SSY TG T V GG T Sbjct: 222 AVPSEMAGAVLYLVSDASSYTTGETLVVDGGLT 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: 138 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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