Align predicted periplasmic glycoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate 353107 BT3581 putative dehydrogenases and relate proteins (NCBI ptt file)
Query= reanno::Btheta:351686 (491 letters) >FitnessBrowser__Btheta:353107 Length = 447 Score = 112 bits (280), Expect = 3e-29 Identities = 86/282 (30%), Positives = 131/282 (46%), Gaps = 26/282 (9%) Query: 5 SRRKFLK---TGAAALAGITIAPSSILGMSHGHVSPTDKLNLAAVGIGGMGHA---NINN 58 +RR F+K G AAL+ +I P + +K+ + +G+ G+A Sbjct: 3 TRRDFIKKTVAGTAALSLGSIIPGFGSNSYQEILGANEKIRIGVIGVNSRGNALAQGFAK 62 Query: 59 VKGTENIVALCDVDWKYAKG-------VFDEFPNAKKYWDYRKMYDEMGKSIDGVIIATA 111 +KG E + LCDVD + + + P +K D RKM + + V+IAT Sbjct: 63 MKGCE-VTYLCDVDSRALERCQADIHKISGRTPKGEK--DIRKMLES--DDFEAVVIATP 117 Query: 112 DHTHAIITADAMTMGKHVYCQKPLTHSVYESRLLTKLAASTGVVTQMGNQGASGEGTDLV 171 DH H AM GKHVY +KP +H+ E+ +L + + Q+GNQ S Sbjct: 118 DHWHGKAAIMAMQAGKHVYLEKPTSHNPAENEMLVRATLKYNRIVQVGNQRRSWPNVIKA 177 Query: 172 CEWIWNGEIGEV--TKVECATDRPIWPQGLNAPEKADRIPNTLNWDLFTGPAKLNP-YNN 228 E I +G IG+V K +RP G P +P+ L+WDL+ GPA P + + Sbjct: 178 IEEIKSGAIGKVRYAKSWYVNNRPSIGTGKVVP-----VPDYLDWDLWQGPAPRVPNFKD 232 Query: 229 VYHPWNWRGWWDYGTGALGDMACHILHQPFRALKLGYPTKVE 270 Y +NW +W++GTG + H + L + YPTKV+ Sbjct: 233 NYIHYNWHWFWNWGTGEALNNGTHFVDILRWGLGVDYPTKVD 274 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: 586 Number of extensions: 33 Number of successful extensions: 3 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: 447 Length adjustment: 33 Effective length of query: 458 Effective length of database: 414 Effective search space: 189612 Effective search space used: 189612 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