Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate WP_086511672.1 BZY95_RS20125 FAD-dependent oxidoreductase
Query= uniprot:Q92LM5 (503 letters) >NCBI__GCF_002151265.1:WP_086511672.1 Length = 570 Score = 172 bits (436), Expect = 3e-47 Identities = 151/499 (30%), Positives = 225/499 (45%), Gaps = 38/499 (7%) Query: 6 IFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFR 65 +FDV ++GGGING A AG+G VAL E DFA TS S+ L+ GG++Y+E +F Sbjct: 15 VFDVLIVGGGINGASAAAALAGKGVRVALIERGDFAGSTSMHSSNLVWGGIKYMESRDFA 74 Query: 66 LVREALMEREVLWAMAPHVIWPMRFVLPFHKG---GPRPAWLIRLGLFLYDHIG-GRKLL 121 LVR+ R L P + +RF+ +G PR W G +LY IG G + Sbjct: 75 LVRKLCRSRNHLIKSYPSTVQEIRFLTTITRGFRYHPRYLW---AGAWLYWLIGNGFTRI 131 Query: 122 PATKTLDMTRDPAGAPLKGLFTKAFEYSDGWV--DDARLVVLNARDAADRGARIMARTRV 179 P + D FEYSD ++ +DAR V R A + GA + Sbjct: 132 PRFLSPQAISDNEAIIDTSSAVGGFEYSDAYLHDNDARFVFNFVRGALNYGAVAVNYVES 191 Query: 180 VSARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGS 239 + ARRE W + +G +R+R+L+NAAGPWVD + + + R+V +G Sbjct: 192 LGARRESDGWLTRVRDVMSGRELEVRSRVLINAAGPWVDEHNALTGQSTNHRHV-YSKGI 250 Query: 240 HIVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDR-----DFTGNPADVRISDA 294 H++V + D R F DGR+ F IP T IGTTD + D+R Sbjct: 251 HLIVPRLTDSQRVLAFFADDGRLFFVIPMGPR-TCIGTTDTRVERPEVVATQEDIRFVLD 309 Query: 295 EIDYLCRAASEYFSDPVGREDIVWTYSAVRPL----FDDGASKAQEATRDYVLRVENGDA 350 I+ R P+ ++DI+ VRPL G + +R + + + + DA Sbjct: 310 NINKRLR-----LERPLDQQDIISIRCGVRPLAVKATGGGERDFLQLSRKHAIDINSHDA 364 Query: 351 PLLNVFGGKLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLR- 409 L++FGGKLT + E++ E + G + H G+ P + + + R Sbjct: 365 H-LSIFGGKLTDCLNVG----EEVVEAVNRMGIEVPFPKHRWYGEPPDQVRREFLHQARL 419 Query: 410 TRYPFLTASH-----ARRLVRLYGTRAAQLLGNAASEADLGKHF--GADLYAAEVDWLIV 462 R LTA + RL R YGT A ++L + + G + E+ + Sbjct: 420 MRLDDLTAQASSEPLSTRLWRRYGTHALEMLEEIREDPRQAEVLIEGTEYLRCELHYAKR 479 Query: 463 QEWALRAEDVLWRRTKLGL 481 +E R ED L RR+K+ L Sbjct: 480 REMITRLEDFLRRRSKIAL 498 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: 674 Number of extensions: 37 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: 570 Length adjustment: 35 Effective length of query: 468 Effective length of database: 535 Effective search space: 250380 Effective search space used: 250380 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 24 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