Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_034528539.1 LOSG293_RS06955 glucose 1-dehydrogenase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000740055.1:WP_034528539.1 Length = 249 Score = 103 bits (258), Expect = 3e-27 Identities = 83/257 (32%), Positives = 126/257 (49%), Gaps = 19/257 (7%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPN-SGGEAQAKKLG-NNCVFAPADV 65 +KG VA+ITGG +G+GL AE V +GA V+ N GG+ ++ G N +F DV Sbjct: 5 LKGKVAIITGGVAGIGLGIAECYVREGAKVVITANHNVEGGKQAVERFGAENALFVQQDV 64 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 E D + + KFG++DV VN AGI + + L+ + + + VNL G Sbjct: 65 AVEADWKKVVDATIEKFGKLDVLVNNAGIGGGGQPI-----EEMPLDAWNKTMSVNLTGN 119 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185 F + + AG + + G G IIN +SVA G YSA+KGG +T +A Sbjct: 120 F--LGVKAGINAMKQTNNG--HGSIINVSSVAGLVGLPMAPDYSATKGGTRLLTHAVALS 175 Query: 186 LA--PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAI--I 241 LA I IRV ++ PG T + +PE + + +P R G+P + + + Sbjct: 176 LAQRKIDIRVNSVHPGWIDTNI---IPEAYRDAILQTIPV-GRFGEPKDIGEICVYLGSE 231 Query: 242 ENPFLNGEVIRLDGAIR 258 E+ + NG +DG +R Sbjct: 232 ESKYANGAEFTVDGGVR 248 Lambda K H 0.318 0.135 0.385 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: 175 Number of extensions: 12 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: 261 Length of database: 249 Length adjustment: 24 Effective length of query: 237 Effective length of database: 225 Effective search space: 53325 Effective search space used: 53325 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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