Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Cola:Echvi_3928 Length = 252 Score = 96.3 bits (238), Expect = 6e-25 Identities = 84/265 (31%), Positives = 124/265 (46%), Gaps = 32/265 (12%) Query: 6 NIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENLLFQKV-------DV 58 ++ GK +VTG +SGIG + +L K + A +T + N+ ++ DV Sbjct: 3 HLNGKVAVVTGGNSGIGYSTAKKL---KEEGAQVIITGRSAEKVNVAAAELGVTGITADV 59 Query: 59 TSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQ 118 ++A+V V FG VD + NAGI +P P GQ D F++ IN Sbjct: 60 LELAAIDAAVNQVKADFGHVDILFVNAGIFLPA-------PIGQTTED--LFDQQMDINL 110 Query: 119 KGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGK 178 KG + L + K G IIN++S G S Y +KAA+ SYTR+ A EL Sbjct: 111 KGAVFTIEKF--LPILKDGGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAP 168 Query: 179 YGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRA-GYASTTTTPLGRSGKLSEV 237 +RV + PG + Y T G + +++ A PL R GK ++ Sbjct: 169 RKIRVNAVNPGPV---------YTPIFSKT-GMSEDQLNGMAAAMQNRIPLKRYGKPEDI 218 Query: 238 ADLVAYYISDRSSYITGITTNVAGG 262 A+LVA+ SDR+S+ITG N+ GG Sbjct: 219 AELVAFLASDRASFITGAEYNIDGG 243 Lambda K H 0.313 0.131 0.361 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: 155 Number of extensions: 12 Number of successful extensions: 5 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: 266 Length of database: 252 Length adjustment: 24 Effective length of query: 242 Effective length of database: 228 Effective search space: 55176 Effective search space used: 55176 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 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