Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate WP_011840947.1 RSPH17029_RS06725 glycerol-3-phosphate dehydrogenase
Query= uniprot:Q92LM5 (503 letters) >NCBI__GCF_000015985.1:WP_011840947.1 Length = 539 Score = 564 bits (1454), Expect = e-165 Identities = 297/515 (57%), Positives = 348/515 (67%), Gaps = 23/515 (4%) Query: 8 DVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFRLV 67 D+F+IGGGINGCGIARDAAGRG SV LAEM D A TSS STKL HGGLRYLE++EFRLV Sbjct: 19 DLFIIGGGINGCGIARDAAGRGLSVTLAEMGDLAQATSSASTKLFHGGLRYLEYFEFRLV 78 Query: 68 REALMEREVLWAMAPHVIWPMRFVLPFHKG---------------------GPRPAWLIR 106 REAL ERE L PH+ WPMRFVLP+ G RPAWLIR Sbjct: 79 REALEERETLLVAMPHISWPMRFVLPWQPEMRFAGDTPTAQLLGRLMPWARGRRPAWLIR 138 Query: 107 LGLFLYDHIGGRKLLPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDA 166 L L YD +GGRK+LP +++D+TRDPAG L+ FTK +EYSD WV+D+RLVVLNARDA Sbjct: 139 LALETYDRLGGRKILPPARSVDLTRDPAGRALQPRFTKGWEYSDCWVEDSRLVVLNARDA 198 Query: 167 ADRGARIMARTRVVSARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVG 226 RGA I+ RT+VV A R G W + E R+ R R LVNA GPWV R++ E + Sbjct: 199 EIRGATILTRTKVVGAERRGDLWHVTTEGAR--GRQVHRVRALVNAGGPWVARIIRETLA 256 Query: 227 NNDVRNVRLVQGSHIVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGNP 286 VRLV+GSHIV K+ FD R YFFQ DGRI+FAIPY+ +FTLIGTTD+D G P Sbjct: 257 LPTTEGVRLVRGSHIVTKRLFDHDRCYFFQGTDGRIIFAIPYETDFTLIGTTDQDHRGAP 316 Query: 287 ADVRISDAEIDYLCRAASEYFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRDYVLRVE 346 + R + E DYLC AS+YF PV REDIVWTYS VRPL DDGA A ATRDYVL ++ Sbjct: 317 DEARCTPEEQDYLCAFASDYFRKPVTREDIVWTYSGVRPLHDDGARSATAATRDYVLSLD 376 Query: 347 NGDAPLLNVFGGKLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVA 406 + APLLNVFGGK+TTYRRLAESA+ K+ E + WTA LPGGDFP G Sbjct: 377 SRGAPLLNVFGGKITTYRRLAESAMAKLAEHFPQARGAWTARVPLPGGDFPWDGAPALAE 436 Query: 407 KLRTRYPFLTASHARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWA 466 LR YPFLT A RLVR YGT A LLG A S DLG+ FGA L AEV WL+ +E+A Sbjct: 437 GLRRDYPFLTERWAMRLVRAYGTDARNLLGPARSALDLGRDFGATLTEAEVRWLMDREYA 496 Query: 467 LRAEDVLWRRTKLGLKFSRAQTAELEEYMRGAVNA 501 RAEDV+WRR+KLGL+ + + A L+ +M+ A A Sbjct: 497 ERAEDVVWRRSKLGLRLTPEEIAALDGWMKDAGGA 531 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: 908 Number of extensions: 36 Number of successful extensions: 4 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: 539 Length adjustment: 35 Effective length of query: 468 Effective length of database: 504 Effective search space: 235872 Effective search space used: 235872 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 10 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