Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate N515DRAFT_2427 N515DRAFT_2427 Predicted dehydrogenases and related proteins
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Dyella79:N515DRAFT_2427 Length = 527 Score = 324 bits (831), Expect = 4e-93 Identities = 206/516 (39%), Positives = 280/516 (54%), Gaps = 87/516 (16%) Query: 5 SRRKFLKTGAAALAGITIAPSSILGMSHGHVSPTDKLNLAAVGIGGMGHANINNVKGTEN 64 SRR+FL A A AG+ I P +LG GH P+D+LN+A +G+GGMG N+ + G EN Sbjct: 30 SRREFLTGTAIAAAGLMIVPRHVLG-GPGHTPPSDRLNIAGIGVGGMGLHNMRALAG-EN 87 Query: 65 IVALCDVDWKYA----KGVFD---------------------------------EFPNAK 87 IVALCDVDW Y +G+ D +F +A+ Sbjct: 88 IVALCDVDWGYTEKSFRGMVDGLPKTQARLDKAQTAKERRELQEEIAQTKLLSGKFNSAR 147 Query: 88 KYWDYRKMYDEMGKSIDGVIIATADHTHAIITADAMTMGKHVYCQKPLTHSVYESRLLTK 147 ++ DYR+M ++ K ID V+IAT DH HA+I + AM+ GKHVY QKPLT S+YE+R L++ Sbjct: 148 RHTDYRRMLEQQ-KDIDAVVIATPDHLHAVIASAAMSHGKHVYLQKPLTWSIYEARELSR 206 Query: 148 LAAS-TGVVTQMGNQGASGEGTDLVCEWIWNGEIGEVTKVECATDRPI--WPQGLNAPEK 204 A +VTQMGNQG S + L+ E+I G IGEV +V T+RP+ WPQG+ P+ Sbjct: 207 KAQDHPKLVTQMGNQGHSTDDARLINEYIAAGAIGEVREVHAWTNRPLAFWPQGIPRPQA 266 Query: 205 --------------ADRI----------PNTLNWDLFTGPAKLNPYNNVYHPWNWRGWWD 240 DR+ P L WDLF GP + Y+ VYHP+NWRGW D Sbjct: 267 RPRPDDASWSEDAVMDRLANAMAGNYPKPEGLVWDLFLGPGPVVDYHPVYHPFNWRGWVD 326 Query: 241 YGTGALGDMACHILHQPFRALKLGYPTKVEGSSTLLLSACAPQAQHVKMIFPARDNMPKV 300 +G GA+GDM H++ PF +L LG+PT VE ST A P A FPAR + P V Sbjct: 327 WGVGAIGDMGAHLIDSPFWSLDLGFPTAVETVSTPFNEASYPMATMTHYEFPARGSRPPV 386 Query: 301 ALPEVEVHWYDGGMMPERPKGFPEGKQLMGPGGGLTIFHGTKDTLICGCYGEQPFLLSGR 360 L WYDG ++P RPKG G Q+ GG ++ G K LI YG P LL Sbjct: 387 KLT-----WYDGALLPPRPKGLGAG-QISKDGG--VLYVGDKGELIHETYGANPRLLPQS 438 Query: 361 VPNA----PKVCRRVTCSHEMDWVRACKEDKSNRVMPKADFSESGPMNEMVVMGVLAIRL 416 + +A P+ R+ SHEM+WV ACK R + FS + + E++++GV+++R Sbjct: 439 LHDAVGTPPQRYARIKTSHEMNWVDACK----GRAEASSPFSYAARLTEVMLLGVVSLRA 494 Query: 417 QGLNKTLEWDGANMCFTNIGD-NETLRTCIKDGFTI 451 G +E+D NM TN+ D N LR +DG+ + Sbjct: 495 GG---RIEYDAENMRITNMPDANAFLRREYRDGWAL 527 Lambda K H 0.319 0.136 0.444 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: 769 Number of extensions: 52 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 491 Length of database: 527 Length adjustment: 34 Effective length of query: 457 Effective length of database: 493 Effective search space: 225301 Effective search space used: 225301 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 (21.8 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