Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate 200162 SO0978 FAD-dependent glycerol-3-phosphate dehydrogenase, family protein (NCBI ptt file)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__MR1:200162 Length = 391 Score = 184 bits (467), Expect = 5e-51 Identities = 132/379 (34%), Positives = 191/379 (50%), Gaps = 22/379 (5%) Query: 15 YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74 YD+A++GGGI+GVGIA AA G S L E+ ++ TS+ SSKLIHGGLRYLE + L Sbjct: 4 YDIAIIGGGISGVGIAQYAAAAGYSTLLIEKGEIGGQTSANSSKLIHGGLRYLESGQINL 63 Query: 75 VREALAEREVLLAKAPHIVKPLRFVLP-HRPHLRPAWMIRAGLFLY------DHLGKREK 127 VR++L ER LL AP +VKP+ F +P ++ R IRAGL LY D LG+ Sbjct: 64 VRKSLLERRNLLDLAPSLVKPVAFYIPVYQDSRRNPLTIRAGLSLYALLSEFDPLGRFVS 123 Query: 128 LPASRGLRFTG--SSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVS 185 +PA RF G S LKA F+Y D DD L A SA+ GAH++ + Sbjct: 124 IPAVHWHRFKGLKLSGLKAV----FQYWDAQTDDKLLTQAVARSAQALGAHIYAEAEFLQ 179 Query: 186 ARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHII 245 K L R G + I + ++NAAGPWV + + I +QG+H++ Sbjct: 180 LNHLKEQIELSF-RHRGEVQQIETKLVINAAGPWVNEVLAHVEPPLAGVEIDWVQGAHLL 238 Query: 246 VPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQV 305 + Y+ D+R++F +P+ + +IGTT+ ++E ET YLL + Sbjct: 239 LDLPAPEGILYLESCFDKRVIFVMPWYGQM-LIGTTETVLTSIDTPPQVTESETQYLLGI 297 Query: 306 VNAHFKQQLAAAD----ILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVF 361 +F + + I+ ++ GVR L S SA R + P LL ++ Sbjct: 298 YCHYFPLSPSIEELKTKIVQTYCGVRVLPKQAS---SAFERPRDTLMQTSISHPRLLCLY 354 Query: 362 GGKLTTYRKLAESALTQLQ 380 GGKLTT+R + L ++ Sbjct: 355 GGKLTTFRSSSAEVLEWIE 373 Lambda K H 0.321 0.136 0.415 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: 433 Number of extensions: 16 Number of successful extensions: 5 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: 512 Length of database: 391 Length adjustment: 33 Effective length of query: 479 Effective length of database: 358 Effective search space: 171482 Effective search space used: 171482 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 (21.8 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