Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate Ga0059261_3265 Ga0059261_3265 Glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__Korea:Ga0059261_3265 Length = 377 Score = 340 bits (873), Expect = 4e-98 Identities = 197/386 (51%), Positives = 240/386 (62%), Gaps = 14/386 (3%) Query: 15 YDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRL 74 YD+ + GGGING IA +A+ GLSV L E+ DLA HTSSASSKLIHGGLRYLE YEFRL Sbjct: 3 YDLLIAGGGINGCAIAREASLLGLSVLLVEKDDLAAHTSSASSKLIHGGLRYLETYEFRL 62 Query: 75 VREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRGL 134 VREAL ERE +LA APH++ P+ FVLPH +RP WM+RAGL+LYD LG LP SR L Sbjct: 63 VREALHERERMLAAAPHLIHPMAFVLPHAHSVRPWWMVRAGLYLYDLLGLGSSLPRSRAL 122 Query: 135 RFTGSSPLKAEIRR---GFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191 R P A I GF Y D VDDA LV NA A +GA V T A R Sbjct: 123 R--RDDPRLAPIAHNVGGFLYWDAQVDDAALVRANAADAVANGAQVETGVAVTGAERGGM 180 Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251 WH+ L +I RA+VNA GPWV F+ D ++ ++ G+RLI+GSHI+VP L+E Sbjct: 181 GWHVFL----SDRRTIDTRAIVNATGPWVKAFL-DTIRIRTTSGLRLIKGSHIVVPALWE 235 Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311 G+HAYILQ DRR+VFA P+ TMIGTTD + P I+ E YL N +F+ Sbjct: 236 GDHAYILQQPDRRVVFATPWRGG-TMIGTTDVPVE-RPEDAGITSAEIDYLCAAANRYFR 293 Query: 312 QQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKL 371 +Q+A AD+ +++G+R L DD DE ITRDY L L + P+LSVFGGK+TT R L Sbjct: 294 RQIAPADVTGTWSGIRALYDDGKDEARTITRDYVLELDTSSA--PILSVFGGKITTARAL 351 Query: 372 AESALTQLQPFFANLGPAWTAKAPLP 397 E AL +L P T PLP Sbjct: 352 GEHALAKLAPALGFTARPVTRDRPLP 377 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: 534 Number of extensions: 24 Number of successful extensions: 6 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: 377 Length adjustment: 32 Effective length of query: 480 Effective length of database: 345 Effective search space: 165600 Effective search space used: 165600 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