Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_041098169.1 SUTH_RS06990 glycerol-3-phosphate dehydrogenase
Query= CharProtDB::CH_091834 (512 letters) >NCBI__GCF_000828635.1:WP_041098169.1 Length = 501 Score = 474 bits (1221), Expect = e-138 Identities = 259/507 (51%), Positives = 324/507 (63%), Gaps = 16/507 (3%) Query: 1 MSQAHTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLI 60 MS PS+P D+ V+GGGING GIA DAAGRG SV L E+ DLA TSSASSKL+ Sbjct: 1 MSADALPSSP---PIDLLVIGGGINGAGIARDAAGRGFSVALVERGDLAGATSSASSKLV 57 Query: 61 HGGLRYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYD 120 HGGLRYLE +EFRLV EALAERE LL APH+V P RF++PH P LRP WMIRAGLFLYD Sbjct: 58 HGGLRYLEQFEFRLVAEALAERETLLRMAPHLVWPARFIMPHVPWLRPRWMIRAGLFLYD 117 Query: 121 HLGKREK---LPASRGLRFTG---SSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHG 174 HLG LP S +R + L+A R GF YSDC DDARLV+ NA A+ G Sbjct: 118 HLGGHHADALLPGSASVRLDRPPYDAGLQARYRHGFIYSDCRTDDARLVIANARDAQRLG 177 Query: 175 AHVHTRTRCVSARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPY 234 A + RT V+ARR G W G+ ++RARA+ N AGPWV + L S Sbjct: 178 ARILPRTELVAARRVDGFWQARF----GNGETLRARAIANVAGPWVKDVLNQRLGVPSTD 233 Query: 235 GIRLIQGSHIIVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAI 294 +RL++GSH+++P+LY GEHA+ILQN+DRR+VF IP+ RFT++GTTD GDP Sbjct: 234 SVRLVRGSHLVLPRLYAGEHAFILQNDDRRVVFMIPWEGRFTLLGTTDVVETGDPLHPQA 293 Query: 295 SEEETAYLLQVVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGE 354 + EE AYL + +Q D + +AGVRPL DD S +PSAITRDYTL L G+G+ Sbjct: 294 TAEEAAYLCAAAGRYLRQAPRPQDAVWRYAGVRPLYDDGSGDPSAITRDYTLRLD-GDGQ 352 Query: 355 PPLLSVFGGKLTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQS--VEALTEQL 412 P+LSVFGGKLTTYR+LAE + +L PAWT + LPGG S + + ++ Sbjct: 353 APVLSVFGGKLTTYRRLAEQVVDKLAATLGARRPAWTEASTLPGGAMPASGLDDFVRREI 412 Query: 413 ANRYAWLDRELALRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQD 472 A RY WL AR +G+ + LL G DLGE GGGL RE++++ EWA Sbjct: 413 APRYPWLAEAQRDALARRHGSELPDLLGAARGPDDLGEDFGGGLCERELEWMLAREWAHS 472 Query: 473 AEDILWRRSKLGLFLSPSQQVRLGQYL 499 A+DILWRRSK GL ++P Q+ R+G++L Sbjct: 473 ADDILWRRSKCGLHMTPEQRERVGRWL 499 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: 790 Number of extensions: 40 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 Apr 09 2024. 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