Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate 5208288 Shew_0800 FAD dependent oxidoreductase (RefSeq)
Query= uniprot:Q92LM5 (503 letters) >FitnessBrowser__PV4:5208288 Length = 413 Score = 190 bits (483), Expect = 7e-53 Identities = 137/384 (35%), Positives = 195/384 (50%), Gaps = 20/384 (5%) Query: 8 DVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFRLV 67 D+ VIGGGI G GIA+ GYSV L E + TSS S+KLIHGGLRYLE + LV Sbjct: 5 DLVVIGGGITGVGIAQCVQAAGYSVVLLEKDNLGEKTSSNSSKLIHGGLRYLESGQLGLV 64 Query: 68 REALMEREVLWAMAPHVIWPMRFVLPFHKGGPRPAWLIRLGLFLY------DHIGGRKLL 121 R++L ER+ L +AP ++ P+ F +P ++G R IR GL LY D +G + + Sbjct: 65 RQSLSERKALLTLAPELVKPVPFYIPIYRGSQRGPLAIRAGLSLYALLSELDPLGQFQSV 124 Query: 122 PATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVVS 181 PA++ ++ AG LKGL F Y D DD L A+ A GA ++ T+V Sbjct: 125 PASRWSEL----AGLKLKGL-RAVFRYWDAQTDDGALTRAVAQSARALGAELL--TQVSL 177 Query: 182 ARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGSHI 241 + E + + + G + +R ++NA GPWV++ L +V V LVQGSH+ Sbjct: 178 EQIEHRPDSCIVSFSHKGETRRLSSRCVINATGPWVNQTLERVTPKVEVSPVELVQGSHL 237 Query: 242 VVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGNPADVRISDAEIDYLCR 301 V+ Y D R++F +P+Q + T+IGTT+ A ++ AE YL Sbjct: 238 VLDIPAPSGIFYLESIFDKRVVFVMPWQGK-TMIGTTETPIDAVDA-AGVTPAEEAYLLG 295 Query: 302 AASEYF----SDPVGREDIVWTYSAVRPLFDDGASKAQEATRDYVLRVENGDAPLLNVFG 357 YF +D E I Y VR L G +A + RD ++ + LL V+G Sbjct: 296 IYRHYFPLSENDGALEERITGRYCGVRVLPKQG-GEAFDLPRDTMMLSRDTHPNLLTVYG 354 Query: 358 GKLTTYRRLAESALEKIGETIGEK 381 GKLTT+R A+ AL + G K Sbjct: 355 GKLTTFRHTAKEALAWVKNRRGPK 378 Lambda K H 0.321 0.137 0.417 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: 445 Number of extensions: 20 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: 503 Length of database: 413 Length adjustment: 33 Effective length of query: 470 Effective length of database: 380 Effective search space: 178600 Effective search space used: 178600 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: 51 (24.3 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