Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_011650427.1 RL_RS03425 L-iditol 2-dehydrogenase
Query= reanno::WCS417:GFF2259 (257 letters) >NCBI__GCF_000009265.1:WP_011650427.1 Length = 262 Score = 270 bits (691), Expect = 2e-77 Identities = 136/255 (53%), Positives = 176/255 (69%) Query: 3 RLEGKSALITGSARGIGRAFAQAYIAEGATVAIADIDLQRAQATAAELGPQAYAVAMDVT 62 RL GK AL+TG A GIG+A + + AEGA V +AD+D +R A +GPQA+ VA+DVT Sbjct: 8 RLSGKVALVTGGASGIGKAVCERFAAEGARVVVADLDGERCARVAEAIGPQAWGVALDVT 67 Query: 63 DQASIDGAITAVVAQAGKLDILINNAALFDLAPIVDITRDSYDRLFSINVAGTLFTLQAA 122 Q SI+ A +A A ++DIL+N A ++D+ I++I+R+ R+F +N+ G +F QA Sbjct: 68 SQDSIEEAARFTIATASQIDILVNAAGIYDVESILEISRERTARVFQVNIEGLIFMTQAV 127 Query: 123 ARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGINVNAIA 182 AR M+ +G GG+IIN +SQAGRRGE YCA+KAAVIS+TQS L LI+ GINVNAIA Sbjct: 128 ARHMVERGEGGRIINFSSQAGRRGEGPAVAYCASKAAVISITQSCALELIRYGINVNAIA 187 Query: 183 PGVVDGEHWDGVDALFAKHEGLAPGEKKQRVGAEVPFGRMGTAEDLTGMAIFLASKEADY 242 PGVVD WD VDA EGL PG+ K+RV A VP GR G ++ MA FLA +A Y Sbjct: 188 PGVVDTPMWDVVDAKLGSREGLRPGDVKRRVAAAVPAGRFGAPQEQAAMAAFLAGPDAAY 247 Query: 243 VVAQTYNVDGGNWMN 257 +VAQ YNVDGGN M+ Sbjct: 248 IVAQCYNVDGGNVMS 262 Lambda K H 0.318 0.133 0.374 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: 219 Number of extensions: 4 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: 257 Length of database: 262 Length adjustment: 24 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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