Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate Pf1N1B4_769 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_769 Length = 486 Score = 750 bits (1937), Expect = 0.0 Identities = 362/486 (74%), Positives = 421/486 (86%) Query: 27 VGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRLVREALAEREVLL 86 VGIAADAAGRGLSVFLCE+ DLA HTSSASSKLIHGGLRYLEHYEFRLVREALAEREVLL Sbjct: 1 VGIAADAAGRGLSVFLCEKDDLASHTSSASSKLIHGGLRYLEHYEFRLVREALAEREVLL 60 Query: 87 AKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGLRFTGSSPLKAEI 146 AKAPHIVK +RFVLPHRPHLRPAWMIRAGLFLYD+LGKREKL S+ L+F S LK+EI Sbjct: 61 AKAPHIVKQMRFVLPHRPHLRPAWMIRAGLFLYDNLGKREKLEGSKSLKFGPDSALKSEI 120 Query: 147 RRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKGLWHLHLERSDGSLYS 206 +GFEYSDC VDDARLVVLNA++ARE GAHVHT+TRCVSARR+KGLWHL+LER+DGSL+S Sbjct: 121 TKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTQTRCVSARRTKGLWHLNLERADGSLFS 180 Query: 207 IRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYEGEHAYILQNEDRRIV 266 IRA+ALVNAAGPWVA+FI+DDLK +SPYGIRLIQGSH+IVPKLYEGEHA+ILQNED+RIV Sbjct: 181 IRAKALVNAAGPWVAKFIRDDLKMESPYGIRLIQGSHLIVPKLYEGEHAHILQNEDQRIV 240 Query: 267 FAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFKQQLAAADILHSFAGV 326 F IPYL+ FT+IGTTDREY GDPA VAI+E ET YLL+VVNAHFK+Q++ DILHS++GV Sbjct: 241 FTIPYLNHFTLIGTTDREYTGDPAAVAITEGETDYLLKVVNAHFKKQISRDDILHSYSGV 300 Query: 327 RPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKLAESALTQLQPFFANL 386 RPLC+DESD PSA+TRDYTL+LS E PLLSVFGGKLTTYRKLAESAL QL P+FA++ Sbjct: 301 RPLCNDESDNPSAVTRDYTLALSGSAEEAPLLSVFGGKLTTYRKLAESALAQLAPYFAHI 360 Query: 387 GPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELALRWARTYGTRVWRLLDGVNGEA 446 P+WTA A LPGGE M + +AL+ ++ +++ W+ E+A RWA TYG+R WR+L+GV Sbjct: 361 KPSWTASATLPGGEDMTTPQALSSRIRDKFDWVPTEIARRWATTYGSRTWRMLEGVESLN 420 Query: 447 DLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSPSQQVRLGQYLQSEHPHR 506 DLGEH+GGGLY REVDYLC EWA A DILWRR+KLGLF +P++Q +L YL +R Sbjct: 421 DLGEHIGGGLYTREVDYLCSEEWATTAHDILWRRTKLGLFTTPAEQQKLEDYLNKVEQNR 480 Query: 507 PRVHAA 512 ++ AA Sbjct: 481 SKIEAA 486 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: 870 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: 486 Length adjustment: 34 Effective length of query: 478 Effective length of database: 452 Effective search space: 216056 Effective search space used: 216056 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