Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate 352997 BT3470 putative dehydrogenase (NCBI ptt file)
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Btheta:352997 Length = 460 Score = 176 bits (445), Expect = 2e-48 Identities = 139/456 (30%), Positives = 207/456 (45%), Gaps = 57/456 (12%) Query: 16 ALAGITIAPSSILGMS--HGHVSPTDKLNLAAVGIGGMGHANINNVK--GTENIVALCDV 71 A AG+ IL + +K+ +A VGIG G I + G +VALCDV Sbjct: 2 ASAGLAAGAGEILNAQTLSSSKNKNEKVKIAYVGIGNRGQQIIEDFARTGMVEVVALCDV 61 Query: 72 DW--KYAKGVFDEFPNAKKYWDYRKMYDEMGKSIDGVIIATADHTHAIITADAMTMGKHV 129 D K+ + V +P AK++ D+R+M+D+ GK D V IAT DH+H I+ A+ GKHV Sbjct: 62 DMGAKHTQKVIGMYPKAKQFRDFRQMFDKAGKEFDAVAIATPDHSHFPISMLALASGKHV 121 Query: 130 YCQKPLTHSVYESRLLTKLAAS-TGVVTQMGNQGASGEGTDLVCEWIWNGEIGEVTKVEC 188 Y +KPL + YE+ LL + A + TQ+GNQG S W+ G I +VT V Sbjct: 122 YVEKPLARTFYEAELLMQAALKRPNLATQVGNQGHSEANYFQFKAWMDAGIIKDVTAVTA 181 Query: 189 ATDR----PIWPQGLNAPEKADRIPNTLNWDLFTGPAKLNPYNNVYHPWNWRGWWDYGTG 244 + W + ++P ++WD + G + YN YH WR W+D+G G Sbjct: 182 HMNNVRRWHKWDTNIYKLPSGQQLPKDMDWDTWLGAVPYHEYNEKYHQGEWRCWYDFGMG 241 Query: 245 ALGDMACHILHQPFRALKLGYPTKVEGSSTLLLSA-----CAPQAQHVKMIFPARDNMPK 299 ALGD HIL L+LG P +V TLL P + + FP R M Sbjct: 242 ALGDWGAHILDTVHEFLELGLPYEV----TLLHEKGHNDYFFPYSSTILFRFPQRKGM-- 295 Query: 300 VALPEVEVHWYDG-GMMPERPKGF---------PEGKQ------LMGPG-----GGLTIF 338 P V++ WYDG +P P G+ P Q + PG LT Sbjct: 296 ---PPVDITWYDGLDNLPPIPAGYGVSGLDPNIPTTNQGDVPAAKLNPGKIIYTKDLTFK 352 Query: 339 HGTKDTLICGCYGEQPFLLSGRVPNAPKVCRRVTCSHEMDWVRACKEDKSNRVMPKADFS 398 G+ + + E+ ++ ++P PK +H +++ AC + R + F Sbjct: 353 GGSHGSTLSIIPEEKAKEMADKLPQIPK----SPSNHFENFLLACNGIEKTR----SPFE 404 Query: 399 ESGPMNEMVVMGVLAIRLQGLNKTLEWDGANMCFTN 434 +G ++++ +GV+A Q LN L +D TN Sbjct: 405 INGVLSQVFSLGVMA---QRLNTQLFFDSRTKQITN 437 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: 622 Number of extensions: 33 Number of successful extensions: 5 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: 491 Length of database: 460 Length adjustment: 33 Effective length of query: 458 Effective length of database: 427 Effective search space: 195566 Effective search space used: 195566 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: 51 (24.3 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