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_084200485.1 C0029_RS02360 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_002869505.1:WP_084200485.1 Length = 257 Score = 240 bits (613), Expect = 2e-68 Identities = 139/257 (54%), Positives = 167/257 (64%), Gaps = 6/257 (2%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLG-NNCVFAPADVT 66 + G VA++TGGASGLG T E V +GA + DL +A LG +N F +V Sbjct: 3 LNGKVAIVTGGASGLGQGTVEAYVAKGAKVAIFDLNAERAQAVVDNLGADNVAFWSVNVA 62 Query: 67 SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126 E +V+TA+A KFG + V N AGI A+KTY KKG +E + V+ +NL GTF Sbjct: 63 DENNVRTAIAEVVEKFGAIHVVNNFAGIGSAAKTYG-KKG-VFPIEQWDPVIAINLTGTF 120 Query: 127 NVIRLVAGEMGQNEP--DQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184 NV R A +M +NE D GG RGVIINTASVA +EGQVGQ AYSA+KGG++GMT+P+AR Sbjct: 121 NVSRYAAEQMSRNEQINDDGG-RGVIINTASVAGYEGQVGQVAYSATKGGVIGMTVPMAR 179 Query: 185 DLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENP 244 DLA GIRV TI PGL TPL SLPE L + V +P RLG PAE AHL I EN Sbjct: 180 DLAGYGIRVNTIVPGLIHTPLFESLPEPAYKSLEASVCYPQRLGKPAEIAHLSVFIAEND 239 Query: 245 FLNGEVIRLDGAIRMQP 261 +LN E IRLDGAIRMQP Sbjct: 240 YLNAECIRLDGAIRMQP 256 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: 211 Number of extensions: 12 Number of successful extensions: 4 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: 257 Length adjustment: 24 Effective length of query: 237 Effective length of database: 233 Effective search space: 55221 Effective search space used: 55221 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