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_009561373.1 RSPH17029_RS19800 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000015985.1:WP_009561373.1 Length = 253 Score = 234 bits (596), Expect = 2e-66 Identities = 128/249 (51%), Positives = 164/249 (65%), Gaps = 4/249 (1%) Query: 13 AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72 A++TG SGLG ATA L GA LLD EA A ++G + DV S + + Sbjct: 8 ALVTGAGSGLGEATARALAAAGARVALLDFNLPAAEAVAAEIGGLAI--GCDVASAESAE 65 Query: 73 TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLV 132 A+A A + G + VNCAG+A A K L + LE+F+R ++VNL+G+FN++RL Sbjct: 66 AAVARAAAEQGVARILVNCAGVAPAKKM--LGRAGVMPLEEFRRTVEVNLVGSFNLLRLF 123 Query: 133 AGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIR 192 A + P + G+RGV I+TASVAA+EGQ+GQ AY+ASKGGIVG+TLP AR+LAP+GIR Sbjct: 124 AAGAAELAPLETGERGVAIHTASVAAWEGQIGQTAYAASKGGIVGLTLPAARELAPLGIR 183 Query: 193 VMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIR 252 V IAPG+F T +L LPE L + VPFPSRLG PAE+A L I+ NP LNGE IR Sbjct: 184 VCAIAPGIFETAMLKGLPEAAQESLGAAVPFPSRLGRPAEFAALALHILSNPMLNGETIR 243 Query: 253 LDGAIRMQP 261 LDGA+RM P Sbjct: 244 LDGALRMAP 252 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: 221 Number of extensions: 11 Number of successful extensions: 2 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: 253 Length adjustment: 24 Effective length of query: 237 Effective length of database: 229 Effective search space: 54273 Effective search space used: 54273 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 Apr 10 2024. 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