Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate CA265_RS13715 CA265_RS13715 glucose dehydrogenase
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__Pedo557:CA265_RS13715 Length = 248 Score = 91.3 bits (225), Expect = 2e-23 Identities = 76/246 (30%), Positives = 126/246 (51%), Gaps = 19/246 (7%) Query: 22 VVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFPCNLMNLE 81 ++ITG +GIG A+ F+ QG V ++ A E + L+ + + + ++ + Sbjct: 6 IIITGASTGIGRAIAALFLKQGHNVV-INSANESN--LIRAFNELGAQHQLA---MVAGD 59 Query: 82 ALRATFTE--IETVM---GGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFCAQ 136 +AT + +ET + G VD+L+NNA + +V A+ D L +NL+ FF +Q Sbjct: 60 ISKATTGQLLVETAVARFGTVDVLVNNAGIFEPKAFLEVDEAHLDSFLNINLKGTFFTSQ 119 Query: 137 AVLPGMRERKGGVILNFGS--ISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVN 194 A + M ++ GG I+N G+ + +G T +++K GI +T +A +FG++ +RVN Sbjct: 120 AAIAQMLKQDGGSIINIGTVLVDHAIGGFPATAPISSKGGIHALTKQLAAEFGKNNIRVN 179 Query: 195 AIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPVRV-DPHDVAALALFLSSDSGAKCTGRE 253 I PG IR+P Q A LA L R+ + DVA LAL+L+ + TG Sbjct: 180 GIAPGIIRSPLQE---KNGISNADDLAGLHLLNRIGETQDVAQLALYLAESNFV--TGEI 234 Query: 254 YYVDAG 259 +D G Sbjct: 235 INLDGG 240 Lambda K H 0.322 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: 167 Number of extensions: 11 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: 263 Length of database: 248 Length adjustment: 24 Effective length of query: 239 Effective length of database: 224 Effective search space: 53536 Effective search space used: 53536 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: 47 (22.7 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