Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate PfGW456L13_2058 Short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2058 Length = 253 Score = 111 bits (277), Expect = 2e-29 Identities = 87/270 (32%), Positives = 134/270 (49%), Gaps = 31/270 (11%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELLS--LKVKVANFDLTDNGEKHENLL--------FQ 54 + +G+ V+VTG ++GIG+A + LKV VA+ D+ GE L+ F Sbjct: 3 MTFSGQVVVVTGGAAGIGRATAQAFAAEGLKVVVADMDVA-GGEGTVALIRTAGGEATFV 61 Query: 55 KVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKIT 114 + +VT V+ + V+ +G +D NNAGI I K + LD+ F+ I Sbjct: 62 RCNVTLESDVKNLMEEVINTYGRLDYAFNNAGIEIE------KGKLAEGTLDE--FDAIM 113 Query: 115 MINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAK 174 +N KG++L + LL+A+ G I+N AS AGL + S YA +K AV T+S A Sbjct: 114 GVNVKGVWLCMKYQLPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAI 173 Query: 175 ELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKL 234 E K +RV + P +++ T + AYE + + G + P+GR GK+ Sbjct: 174 EYAKKKIRVNAVCPAVID-TDMFRRAYE-----------ADPKKGEFANAMHPVGRIGKV 221 Query: 235 SEVADLVAYYISDRSSYITGITTNVAGGKT 264 E+A V Y SD +++ TG + V GG T Sbjct: 222 EEIASAVLYLCSDGAAFTTGHSLAVDGGVT 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: 168 Number of extensions: 8 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