Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 150 bits (378), Expect = 7e-41 Identities = 90/244 (36%), Positives = 142/244 (58%), Gaps = 6/244 (2%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPSRTLALQVDITKKE 73 +V +VTG A GIG A + F+ G V++ D E ++ A + P A+ +D++ + Sbjct: 33 RVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERADSLGPDHH-AIAMDVSSEA 91 Query: 74 NIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPE--EYWDKTMELNLKGSFLMAQIIG 131 I + ++ + + ++D+L N+AGV + L + E + +N+ G+FL A+ G Sbjct: 92 QIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTGAFLAAREAG 151 Query: 132 REMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISPT 191 R MI G G I+N+AS A ++AL K +Y ASKAA++S+T+ LA EWA + VNA+ P Sbjct: 152 RLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKGVRVNAVLPG 211 Query: 192 VILTELGK-KAWAGQVGED-MKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIIDG 249 T++ + + AG + + IP GR G PEE+A A FL SDAAS + G L++DG Sbjct: 212 YTRTQMVQDQIDAGLLDPSIVLSRIPLGRMGEPEEMAEGAFFLASDAASYVVGATLVVDG 271 Query: 250 GYTI 253 GYT+ Sbjct: 272 GYTV 275 Score = 126 bits (317), Expect = 8e-34 Identities = 82/246 (33%), Positives = 127/246 (51%), Gaps = 15/246 (6%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDITKKEN 74 +V+ +TG GIG+ + +LF G +++++ + A+ + +Q DIT Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQADITDVAA 355 Query: 75 IEKVVAEIKKVYPKIDILANSAGVA------LLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128 +E A+ + + ++D+L N+AG A L + A+D Y +LN G A+ Sbjct: 356 VEAAFAQAQARWGRLDVLINNAGAADVFKPSLEQTAQDFTSVY-----DLNFSGPLATAK 410 Query: 129 IIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188 R M + GG IVN+ S A + AL + AYCA+KAA+ M++ LA EWA I VN + Sbjct: 411 AAARLM--SQGGVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNTV 468 Query: 189 SPTVILTE--LGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLI 246 +P I T L K+ + +++ P GR G P EVA FL S AAS + G L Sbjct: 469 APGYIETPAVLALKSAGRAQFDKIRRRAPIGRLGDPMEVARTIAFLASPAASYVAGATLT 528 Query: 247 IDGGYT 252 +DGG+T Sbjct: 529 VDGGWT 534 Lambda K H 0.316 0.133 0.369 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: 311 Number of extensions: 19 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 254 Length of database: 546 Length adjustment: 30 Effective length of query: 224 Effective length of database: 516 Effective search space: 115584 Effective search space used: 115584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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