Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate GFF1639 HP15_1598 FAD dependent oxidoreductase
Query= uniprot:Q92LM5 (503 letters) >FitnessBrowser__Marino:GFF1639 Length = 532 Score = 218 bits (555), Expect = 4e-61 Identities = 175/504 (34%), Positives = 258/504 (51%), Gaps = 47/504 (9%) Query: 7 FDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFRL 66 FDV V+GGGI G G+AR+AAG G L E DF+ GTSS S+K++HGGLRYL + L Sbjct: 17 FDVVVVGGGITGAGVAREAAGSGLRTLLVEQKDFSWGTSSRSSKMVHGGLRYLGSGHYGL 76 Query: 67 VREALMEREVLWAMAPHVIWPMRFVLPFHKG---GPRPAWLIRLGLFLYDHIG---GRKL 120 R+A+ ERE L A AP +I P+RF++P KG GPR L + L +YD I R Sbjct: 77 TRDAVRERERLMAEAPGLIEPLRFIMPHFKGQFPGPR---LFQTLLRVYDLIARNQSRHF 133 Query: 121 LPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVV 180 L +++ L G A ++D DD+RLV+ +A GA + TR Sbjct: 134 LTPAESMLWVPGLTSENLAG----ASGFTDAVTDDSRLVLRLIAEARRDGAMCLNYTRAD 189 Query: 181 SARREGGRWA-IEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGS 239 +R G + + I++ E + A +++NA G W DR+ S + D ++R ++GS Sbjct: 190 EIKRSNGDVSGLLIQAEENDTPIEVFAPLVINATGAWADRLQSSKT-SEDAMHIRPLRGS 248 Query: 240 HIVV--KKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGN-PADVRISDAEI 296 H+V+ F DGR +FA P+ T++GTTD D G+ + IS++E Sbjct: 249 HLVLPWSSLPVSCSVSLFHPEDGRPVFAFPWLGT-TVLGTTDIDHEGSLDQEPVISESET 307 Query: 297 DYLCRAASEYF-SDPVGREDIVWTYSAVRPLFDDGASKA-QEATRDYVLRVENGDAPLLN 354 YL AS F P+ R DI+ T++ VRP+ DG K+ + R++ LRV+ G L++ Sbjct: 308 AYLLEIASRLFPGSPITRNDILSTWAGVRPVVTDGTGKSPSKENREHALRVDRG---LVS 364 Query: 355 VFGGKLTTYRRLAESAL-EKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLRTRYP 413 + GGKLTT+R +A AL + +GE E R PA+ + RT +P Sbjct: 365 IAGGKLTTFRVIAREALVQGLGEGSSEVLR-------------PAS----KPVFQRTDHP 407 Query: 414 FLTASHA----RRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRA 469 A+ + +RL YG Q+L + E + + DL AE+ W +E Sbjct: 408 SRPATISYQCWQRLQGFYGPELDQMLASGPLE-PVTPNRATDLLWAELCWACRREDVQHL 466 Query: 470 EDVLWRRTKLGLKFSRAQTAELEE 493 +D+L RRT+LG+ A A L E Sbjct: 467 DDLLLRRTRLGMVLPNAGEALLPE 490 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: 668 Number of extensions: 36 Number of successful extensions: 6 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: 532 Length adjustment: 35 Effective length of query: 468 Effective length of database: 497 Effective search space: 232596 Effective search space used: 232596 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: 52 (24.6 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