Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate PP_1073 PP_1073 glycerol-3-phosphate dehydrogenase (aerobic)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__Putida:PP_1073 Length = 514 Score = 747 bits (1929), Expect = 0.0 Identities = 367/512 (71%), Positives = 422/512 (82%) Query: 1 MSQAHTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLI 60 +SQ + P A YD+AV+GGGINGVGIAADAAGRGL VFLCE+ DLAQHTSSASSKLI Sbjct: 3 VSQPVSSQPPTANCYDLAVIGGGINGVGIAADAAGRGLKVFLCEKDDLAQHTSSASSKLI 62 Query: 61 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYD 120 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKP+RFVLPHRPHLRPAWMIRAGLFLYD Sbjct: 63 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPMRFVLPHRPHLRPAWMIRAGLFLYD 122 Query: 121 HLGKREKLPASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTR 180 HLGKR++L ASR LRF PLK I RGFEY+DCAVDDARLVVLNA++ARE GAH+ TR Sbjct: 123 HLGKRKRLGASRSLRFGPGYPLKPAITRGFEYADCAVDDARLVVLNAMAARELGAHIRTR 182 Query: 181 TRCVSARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQ 240 TRC+ A R +GLW + L+ +DGSL +I ARALVNAAGPWVA FI+DDLK +PYGIRLIQ Sbjct: 183 TRCLRAERVEGLWQVELQHADGSLQTIHARALVNAAGPWVASFIKDDLKLDAPYGIRLIQ 242 Query: 241 GSHIIVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETA 300 GSHIIVP+LYEGEHAYILQNED+RIVF IPYLDRFT+IGTTDREY GDPA VAI+E+ET Sbjct: 243 GSHIIVPRLYEGEHAYILQNEDQRIVFCIPYLDRFTLIGTTDREYSGDPAAVAITEQETH 302 Query: 301 YLLQVVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSV 360 YLL+VVN HF QL+ ADILH+++GVRPLC+DESD PSA+TRDYTL+LSA G+ PLLSV Sbjct: 303 YLLKVVNEHFNHQLSQADILHTYSGVRPLCNDESDNPSAVTRDYTLALSAEVGQAPLLSV 362 Query: 361 FGGKLTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLD 420 FGGKLTTYRKLAESA+ +L+PFF + WTA APLPG E M +V+AL + + R WL Sbjct: 363 FGGKLTTYRKLAESAMAELKPFFTQMRAPWTASAPLPGAEGMTTVQALIDAVLARCGWLP 422 Query: 421 RELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRR 480 +LA RW TYG+RVWRLLDGV+G DLG+ +G GL+ REVDYL + EWA+ DI+WRR Sbjct: 423 VDLAKRWVLTYGSRVWRLLDGVHGPEDLGQAIGAGLFTREVDYLLEEEWAEQTADIIWRR 482 Query: 481 SKLGLFLSPSQQVRLGQYLQSEHPHRPRVHAA 512 +KLGL L+ +Q+ L YLQ R AA Sbjct: 483 TKLGLSLTAQEQMALEAYLQQARKVRANSRAA 514 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: 842 Number of extensions: 23 Number of successful extensions: 1 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: 514 Length adjustment: 35 Effective length of query: 477 Effective length of database: 479 Effective search space: 228483 Effective search space used: 228483 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: 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