Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate WP_015887820.1 NGR_RS08385 glycerol-3-phosphate dehydrogenase
Query= uniprot:Q92LM5 (503 letters) >NCBI__GCF_000018545.1:WP_015887820.1 Length = 503 Score = 525 bits (1352), Expect = e-153 Identities = 271/504 (53%), Positives = 339/504 (67%), Gaps = 3/504 (0%) Query: 1 MSEQTIFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLE 60 MS+ +D+FVIGGGING GIARDAAGRG SV L E D A GTSS S KL+HGGLRYLE Sbjct: 1 MSDTRTYDLFVIGGGINGAGIARDAAGRGLSVLLCEKDDLAQGTSSRSGKLVHGGLRYLE 60 Query: 61 HYEFRLVREALMEREVLWAMAPHVIWPMRFVLPFHKGGPRPAWLIRLGLFLYDHIGGRKL 120 +YEFRLVREAL+EREVL APH+IWPMRFVLP H RPAWL+RLGL LYDH+GGRK Sbjct: 61 YYEFRLVREALIEREVLLQSAPHIIWPMRFVLP-HNPVDRPAWLVRLGLLLYDHLGGRKR 119 Query: 121 LPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVV 180 LP T+TLD+ P GAP+K + +AFEYSD WVDDARLVVLNA DA RGARI+ RT Sbjct: 120 LPGTRTLDLRTAPEGAPIKPAYRRAFEYSDCWVDDARLVVLNALDAEQRGARILTRTACS 179 Query: 181 SARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGSH 240 + RR G W +E+ TGA+ +RAR +VN AGPWV+ V+ G N R+VRLV+GSH Sbjct: 180 NIRRRGDLWHVEMTDAVTGAKAEVRARCVVNTAGPWVNDVIGRVAGLNSRRSVRLVKGSH 239 Query: 241 IVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGNPADVRISDAEIDYLC 300 IVV K ++ +AY QNPD R++F PYQ++ LIGTTD + G P DV EI YL Sbjct: 240 IVVPKFWEGRQAYLVQNPDKRVIFINPYQNDLALIGTTDIPYDGRPEDVAADADEIAYLV 299 Query: 301 RAASEYFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRDYVLRVE--NGDAPLLNVFGG 358 ++ + YF + DI+ ++S VRPL+DD A TRDY+ ++ NG+APLL+VFGG Sbjct: 300 KSVNRYFKQQLSDADIIQSFSGVRPLYDDNAENPSAVTRDYIFELDAANGEAPLLSVFGG 359 Query: 359 KLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLRTRYPFLTAS 418 K+TT+R+L+E ALE++ + G WTA +HLPGGD A +D + +LR+RY +L A Sbjct: 360 KITTFRKLSEHALERLKPFFPKIGPAWTARAHLPGGDMADADFDRFLGELRSRYRWLPAD 419 Query: 419 HARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRAEDVLWRRTK 478 A+ RLYGTR L+G+A S +LG F E +LI EWA ED+L RRTK Sbjct: 420 LAKHYARLYGTRTHALIGDANSLEELGTAFSRLFREREARFLIETEWARTVEDLLQRRTK 479 Query: 479 LGLKFSRAQTAELEEYMRGAVNAA 502 GL S A+ ++ G AA Sbjct: 480 HGLHMSEAEKRSFSGWLEGQQAAA 503 Lambda K H 0.321 0.137 0.417 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: 747 Number of extensions: 33 Number of successful extensions: 3 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: 503 Length of database: 503 Length adjustment: 34 Effective length of query: 469 Effective length of database: 469 Effective search space: 219961 Effective search space used: 219961 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 (21.9 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