Align L-iditol 2-dehydrogenase (EC 1.1.1.14); D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_012385307.1 BIND_RS11835 NAD(P)-dependent alcohol dehydrogenase
Query= reanno::HerbieS:HSERO_RS17015 (345 letters) >NCBI__GCF_000019845.1:WP_012385307.1 Length = 348 Score = 441 bits (1133), Expect = e-128 Identities = 218/343 (63%), Positives = 267/343 (77%) Query: 1 MQALVLEATRELKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPMV 60 MQALVLE EL LR++DLP +G V+I +HTVGICGSD+HY+THGSIGP+ VE PMV Sbjct: 1 MQALVLERKGELSLRDVDLPLAVGPGQVKIAVHTVGICGSDVHYFTHGSIGPYIVEKPMV 60 Query: 61 LGHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIHG 120 LGHEA+GT++EVG VS LKVGDRVCMEPG+P + S A+ G+YN+DP+V FWATPP+HG Sbjct: 61 LGHEATGTIVEVGPNVSTLKVGDRVCMEPGVPDMSSRASKLGLYNVDPSVTFWATPPVHG 120 Query: 121 CLTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVIGAGTIGAM 180 LT VVHPAAFTY+LP NVSFAEGA+VEP +IG+QAAT+AR+ PGD A VIGAGTIG M Sbjct: 121 VLTPYVVHPAAFTYKLPANVSFAEGALVEPFAIGMQAATRARIAPGDVAAVIGAGTIGIM 180 Query: 181 TALAALAGGAARVILADVVAEKLAHFADNPAVITVDVTRETLTDVVRQATDGWGADVVFE 240 TALAA+AGG +RV ++D EKLA ++ V+ E+L DVV + T+ WGADVVFE Sbjct: 181 TALAAVAGGCSRVFISDFSKEKLAIAGGYDCIVPVNAGEESLADVVARETENWGADVVFE 240 Query: 241 ASGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVFRYANIFPRALA 300 ASG Y L +V PGG VLVG+P PVA DV + +KEVR+E+VFRYANIF RALA Sbjct: 241 ASGSPKAYGDLFRIVRPGGAVVLVGLPVEPVAFDVSSAISKEVRIETVFRYANIFDRALA 300 Query: 301 LISSGMIDVKPFISRKFPFSQSIRAFEEAASGRPQDVKIQIEM 343 LI+SG +++KP I+ FPFS S+ AFE AA+GRP DVK+QIE+ Sbjct: 301 LIASGKVNLKPLITGTFPFSDSVVAFERAAAGRPTDVKLQIEV 343 Lambda K H 0.321 0.137 0.403 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: 407 Number of extensions: 12 Number of successful extensions: 1 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: 345 Length of database: 348 Length adjustment: 29 Effective length of query: 316 Effective length of database: 319 Effective search space: 100804 Effective search space used: 100804 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: 49 (23.5 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