Align L-iditol 2-dehydrogenase (EC 1.1.1.14); D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 3607129 Dshi_0551 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= reanno::HerbieS:HSERO_RS17015 (345 letters) >FitnessBrowser__Dino:3607129 Length = 347 Score = 439 bits (1129), Expect = e-128 Identities = 210/342 (61%), Positives = 269/342 (78%) Query: 2 QALVLEATRELKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPMVL 61 +ALVLEA R+L LR+IDLP ++G +DVRI I TVG+CGSD+HYYTHG IGPF V+ PMVL Sbjct: 3 RALVLEAARKLALRDIDLPDELGPEDVRIAIDTVGVCGSDVHYYTHGKIGPFVVKQPMVL 62 Query: 62 GHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIHGC 121 GHEA+G V E+G+AV+HL +GDRVCMEPGIP S A+ G+YN+DPAV+FWATPP+HGC Sbjct: 63 GHEAAGIVTEIGAAVTHLALGDRVCMEPGIPNGSSKASKLGVYNVDPAVQFWATPPVHGC 122 Query: 122 LTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVIGAGTIGAMT 181 LT SVVHPAAFT++LPD+VSFAEGA+VEP +IG+QAA KAR+KPGD A+V GAG IG M Sbjct: 123 LTPSVVHPAAFTFKLPDHVSFAEGAMVEPFAIGMQAAAKARIKPGDVALVTGAGPIGVMV 182 Query: 182 ALAALAGGAARVILADVVAEKLAHFADNPAVITVDVTRETLTDVVRQATDGWGADVVFEA 241 ALAALAGG A+V ++D+V +KLA A + + + R+ +V+++AT+GWGADVVFE Sbjct: 183 ALAALAGGCAKVFVSDLVEDKLAIAAGYDNIHPILIPRDNPAEVLQEATEGWGADVVFEC 242 Query: 242 SGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVFRYANIFPRALAL 301 +G A Q L+ P GC V VGMP PV +D+V Q++E+R+E+VFRYAN++ RA+AL Sbjct: 243 AGAAASIQAALEAAAPAGCVVWVGMPVDPVPVDIVLAQSRELRMETVFRYANMYDRAIAL 302 Query: 302 ISSGMIDVKPFISRKFPFSQSIRAFEEAASGRPQDVKIQIEM 343 ++SG +D+KP IS FPF SI AF+ A RP DVKIQI+M Sbjct: 303 LASGKVDLKPLISATFPFEDSIAAFDRAVEARPTDVKIQIKM 344 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: 403 Number of extensions: 16 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: 347 Length adjustment: 29 Effective length of query: 316 Effective length of database: 318 Effective search space: 100488 Effective search space used: 100488 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 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