Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_083491969.1 ABB28_RS07835 glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >NCBI__GCF_001431535.1:WP_083491969.1 Length = 501 Score = 500 bits (1287), Expect = e-146 Identities = 262/491 (53%), Positives = 327/491 (66%), Gaps = 9/491 (1%) Query: 16 DVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFRLV 75 DV VVGGGING GIA DAAGR L+V LCEQHDLA HTSSASSKL+HGGLRYLEH +F +V Sbjct: 3 DVLVVGGGINGTGIARDAAGRVLTVALCEQHDLASHTSSASSKLVHGGLRYLEHGQFGMV 62 Query: 76 REALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKRE-KLPASRGL 134 R++L ER VL+ APH+V+PL FVLPH HLRPAW+I GL+LYDHLG R +LP SR L Sbjct: 63 RKSLQERAVLMRIAPHLVQPLPFVLPHEAHLRPAWLIHLGLWLYDHLGGRSPQLPRSRSL 122 Query: 135 RFTG---SSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSKG 191 R G +PL+ ++RRGF Y+D DARLVV+NAI A E GAH+ TRT C A R Sbjct: 123 RLRGHPLGAPLREDLRRGFTYTDAQAPDARLVVVNAIDAAERGAHIWTRTVCEQAWRQAD 182 Query: 192 LWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKLYE 251 W + L DG+ S+R R LVNA G W RF+ +++ +RL+QGSHI+VP LY Sbjct: 183 GWSVDLRDPDGTQRSVRTRMLVNATGAWAPRFV-ENISLTRGVALRLVQGSHIVVPALYA 241 Query: 252 GEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAHFK 311 +HAY+LQ D RIVFA+P+ D +T+IGTTD +++GDP V + + + YL N F+ Sbjct: 242 HDHAYLLQQPDGRIVFALPFEDHYTLIGTTDVDFEGDPGAVHVDDAQRDYLCAAANRSFR 301 Query: 312 QQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYRKL 371 QQ + DI+ F+GVR L DD E SA+TRDY L L A PLL+V GGKLTTYR+L Sbjct: 302 QQTSPRDIVWEFSGVRALLDDPEAEASAVTRDYRLDLDAEGA--PLLNVLGGKLTTYRRL 359 Query: 372 AESALTQLQPFFANLGPAWTAK-APLPGGEQMQSVEALTEQLANRYAWLDRELALRWART 430 AE A+ L PAWTA A LPG E+ + LA ++ WL +LA RW+RT Sbjct: 360 AEEAVDLLAGHAGTAAPAWTATGAQLPGAERGTPAQC-AAWLATQWPWLPPKLAARWSRT 418 Query: 431 YGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSPS 490 YG R +L + A LG H G LY EV YLC HEWA+ A+D+LWRR++LGL L + Sbjct: 419 YGARATLILGQADSLAALGTHFGADLYEAEVRYLCTHEWARQADDVLWRRTRLGLVLDAA 478 Query: 491 QQVRLGQYLQS 501 QQ RL +L + Sbjct: 479 QQHRLACWLDT 489 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: 781 Number of extensions: 32 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: 501 Length adjustment: 34 Effective length of query: 478 Effective length of database: 467 Effective search space: 223226 Effective search space used: 223226 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 24 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