Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate WP_090442219.1 BLS63_RS07815 glycerol-3-phosphate dehydrogenase/oxidase
Query= uniprot:Q92LM5 (503 letters) >NCBI__GCF_900100495.1:WP_090442219.1 Length = 526 Score = 207 bits (527), Expect = 7e-58 Identities = 160/493 (32%), Positives = 247/493 (50%), Gaps = 33/493 (6%) Query: 7 FDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFRL 66 +D+ VIGGGI+G GI R+AA RG+ L E DFA GTSS S+K++HGGLRY+ + +L Sbjct: 21 WDLLVIGGGISGAGILREAARRGWKCLLLEQRDFAWGTSSRSSKMVHGGLRYIARGQLQL 80 Query: 67 VREALMEREVLWAMAPHVIWPMRFVLPFHKGG-PRPAWLIRLGLFLYDHIGGRKLLPATK 125 R+++ ER+ L AP ++ P+ FVLP ++GG P P L L LYD + G++ Sbjct: 81 TRDSVRERQRLLQEAPGLVDPLSFVLPHYRGGFPGPKAFGGL-LTLYDVLAGKRTHRYYP 139 Query: 126 TLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVVSARRE 185 ++ G +GL + D DDARLV+ +A G + +V+ R+ Sbjct: 140 LHELRYLAPGLKEEGLL-GGTRFFDAVTDDARLVLRVIGEARGDGGEALNGVKVLELLRD 198 Query: 186 GGR-WAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGSHIVVK 244 GR + E E+G R T R+R + A G W DR+ + + + +R ++GSH+++ Sbjct: 199 NGRVVGLLAEDRESGRRFTFRSRAVAQATGAWADRLRPK----SGPQQIRPLRGSHLLLP 254 Query: 245 K-KFDDPRAYFFQN-PDGRIMFAIPYQDEFTLIGTTDRDFTGN-PADVRISDAEIDYLCR 301 + A+ F + D R +F P++ T++GTTD D D RIS AE+DYL Sbjct: 255 AWRLPVAHAFSFMHAADRRPVFVFPWEGA-TVVGTTDLDHREPLDQDARISAAELDYLLA 313 Query: 302 AASEYF-SDPVGREDIVWTYSAVRPLFDDGASKAQ--EATRDYVLRVENGDAPLLNVFGG 358 A ++ F S + D+ T++ VRP+ +G S Q + R++ L +E G + + GG Sbjct: 314 ACAQQFPSAAIRARDVRSTWAGVRPVVSEGDSGRQPSDEKREHALWIEPG---CVTLAGG 370 Query: 359 KLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLRTRYPFLTAS 418 KLTT+R LA L+ +G+ + V P P G L+ + Sbjct: 371 KLTTFRLLALEVLQACAGFVGQAVDERGTVVFRPCAALPMPG--------------LSPA 416 Query: 419 HARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRAEDVLWRRTK 478 +RL +G +LL E + +D E+ W E L +D+L RRT+ Sbjct: 417 QQKRLAGRHGRALPELLA-LLDEVGSERVADSDTLWVELAWAAQNELVLHLDDLLLRRTR 475 Query: 479 LGLKFSRAQTAEL 491 LGL + AEL Sbjct: 476 LGLLLAGGGRAEL 488 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: 701 Number of extensions: 34 Number of successful extensions: 7 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: 526 Length adjustment: 35 Effective length of query: 468 Effective length of database: 491 Effective search space: 229788 Effective search space used: 229788 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 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