Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate AZOBR_RS25870 AZOBR_RS25870 glycerol-3-phosphate dehydrogenase
Query= uniprot:Q92LM5 (503 letters) >FitnessBrowser__azobra:AZOBR_RS25870 Length = 513 Score = 607 bits (1566), Expect = e-178 Identities = 304/496 (61%), Positives = 366/496 (73%), Gaps = 7/496 (1%) Query: 6 IFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYEFR 65 ++D+ ++GGGINGCGIARDAAGRG SV L E D ASGTSS STKLIHGGLRYLE+YEFR Sbjct: 4 VYDLAIVGGGINGCGIARDAAGRGCSVYLCEQKDLASGTSSASTKLIHGGLRYLEYYEFR 63 Query: 66 LVREALMEREVLWAMAPHVIWPMRFVLPFHKGGPRPAWLIRLGLFLYDHIGGRKLLPATK 125 LVREAL EREVLW MAPH+IWP+RFVLP H G RP+W +RLGLFLYDH+GGR+ LP T+ Sbjct: 64 LVREALREREVLWRMAPHIIWPLRFVLP-HLPGLRPSWFLRLGLFLYDHLGGREKLPGTR 122 Query: 126 TLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVVSARRE 185 LD+ DPAG PLK F +AFEYSD WVDDARLVVLNA+DAA GA I RTR ++A RE Sbjct: 123 GLDLRNDPAGKPLKPGFGRAFEYSDCWVDDARLVVLNAQDAARMGATIRTRTRFLNAVRE 182 Query: 186 GGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGSHIVVKK 245 G W + +E T +G R ++RAR LVNAAGPWV V+ + + +RLVQGSHIVV K Sbjct: 183 DGLWTVTVEDTRSGQRSSIRARALVNAAGPWVSEVMRQGARSTVDARIRLVQGSHIVVPK 242 Query: 246 KFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGNPADVRISDAEIDYLCRAASE 305 FD R Y FQN D RI+FAIPY+ +FTLIGTTD D+ G+PADVR S+AEI YLC AA + Sbjct: 243 LFDHDRCYIFQNADKRIVFAIPYERDFTLIGTTDNDYQGDPADVRASEAEIAYLCAAAGD 302 Query: 306 YFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRDYVLRVE---NGDAPLLNVFGGKLTT 362 YF+ PV D+VWTYS VRPL+DDGAS AQ ATRDYVL ++ +G A LLN+FGGK+TT Sbjct: 303 YFAKPVTPADVVWTYSGVRPLYDDGASTAQAATRDYVLALDAPGDGKAALLNIFGGKITT 362 Query: 363 YRRLAESALEKIG---ETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLRTRYPFLTASH 419 YRRLA++A+ K+ + W++ LPGGDFPA G +++LR R PFLT H Sbjct: 363 YRRLADAAIAKLAPFLPKLAPGASDWSSAGTLPGGDFPADGVATLISELRGRAPFLTQPH 422 Query: 420 ARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRAEDVLWRRTKL 479 RL R YGTRA ++L +AA DLG+ FG L AEV +L+ +EWA AEDVLWRRTKL Sbjct: 423 LERLARTYGTRARRILDSAARTEDLGRDFGGTLTEAEVRYLMTEEWAETAEDVLWRRTKL 482 Query: 480 GLKFSRAQTAELEEYM 495 GL+ AQ L+ +M Sbjct: 483 GLRLDAAQAQALDAFM 498 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: 856 Number of extensions: 37 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: 513 Length adjustment: 34 Effective length of query: 469 Effective length of database: 479 Effective search space: 224651 Effective search space used: 224651 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 17 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