Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate PfGW456L13_1732 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1732 Length = 528 Score = 782 bits (2020), Expect = 0.0 Identities = 376/512 (73%), Positives = 441/512 (86%) Query: 1 MSQAHTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLI 60 M + P+ PLAEVYD+AV+GGGINGVGIAADAAGRGLSVFLCE+ DLA HTSSASSKLI Sbjct: 17 MPTSTLPTPPLAEVYDIAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLI 76 Query: 61 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYD 120 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVK +RFVLPHRPHLRPAWMIRAGLFLYD Sbjct: 77 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKQMRFVLPHRPHLRPAWMIRAGLFLYD 136 Query: 121 HLGKREKLPASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTR 180 +LGKRE+L S+ L+F S LK+EI +GFEYSDC VDDARLVVLNA++ARE GAHVHT+ Sbjct: 137 NLGKREQLQGSKSLKFGPDSALKSEITKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTQ 196 Query: 181 TRCVSARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQ 240 TRCVSARR+KGLWHLHLER+DGSL+SIRA+ALVNAAGPWVARFI+DDLK +SPYGIRLIQ Sbjct: 197 TRCVSARRTKGLWHLHLERADGSLFSIRAKALVNAAGPWVARFIRDDLKMESPYGIRLIQ 256 Query: 241 GSHIIVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETA 300 GSH+IVPKLYEGEHA+ILQNED+RIVF IPYL+ FT+IGTTDREY GDPAKVAI++ ET Sbjct: 257 GSHLIVPKLYEGEHAHILQNEDQRIVFTIPYLNHFTLIGTTDREYTGDPAKVAITDGETD 316 Query: 301 YLLQVVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSV 360 YLL VVNAHFK+Q++ DILHS++GVRPLC+DESD PSA+TRDYTL+LS E PLLSV Sbjct: 317 YLLNVVNAHFKKQISREDILHSYSGVRPLCNDESDNPSAVTRDYTLALSGTGEEAPLLSV 376 Query: 361 FGGKLTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLD 420 FGGKLTTYRKLAESAL QL P+F ++ P+WTA A LPGGE M + +AL+ ++ +++ W+ Sbjct: 377 FGGKLTTYRKLAESALAQLAPYFKHIQPSWTASATLPGGEDMTTPQALSSRIRDKFDWVP 436 Query: 421 RELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRR 480 ++A RWA +YG+R WR+L+GV +D+GEH+GGGLY REVDYLC EWA A DILWRR Sbjct: 437 SDIARRWATSYGSRTWRMLEGVQDLSDMGEHIGGGLYTREVDYLCSEEWATTAHDILWRR 496 Query: 481 SKLGLFLSPSQQVRLGQYLQSEHPHRPRVHAA 512 SKLGLF + ++Q +L YL +R ++ AA Sbjct: 497 SKLGLFTTAAEQEKLKDYLNKIEQNRNKIEAA 528 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: 932 Number of extensions: 28 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: 528 Length adjustment: 35 Effective length of query: 477 Effective length of database: 493 Effective search space: 235161 Effective search space used: 235161 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