Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 7023065 Shewana3_0303 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__ANA3:7023065 Length = 253 Score = 118 bits (295), Expect = 1e-31 Identities = 90/268 (33%), Positives = 137/268 (51%), Gaps = 34/268 (12%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTD----- 59 + L K VTG A GIG AI+ +LLA+GA V D+ + +N +P D Sbjct: 1 MRLLNKTAVVTGAAGGIGQAIIRKLLAEGARVVAADLSA----DALKVFNDFPADKLVTF 56 Query: 60 ---ISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMV 116 ++ +V V H +FG++D L+NNAG+ + L+ +N+ FE + Sbjct: 57 SVDVTDYKQVEAMVKHAADQFGQLDILINNAGIGLAKPLLQHDP------IND--FEPVT 108 Query: 117 NINQKGVFLMSQAVARQMVKQRS-GVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWS 175 N+NQKGV+ A RQ Q S GVI+N SS SE Y +KAA++ T+ + Sbjct: 109 NVNQKGVYHGILAGGRQFQAQGSRGVILNTSSVYAQIASEMTFTYNVSKAAVDMMTKCAA 168 Query: 176 KELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRL 235 EL G+RV VAPG ++ LR +Y EAL +I EQ+R+ +++ + Sbjct: 169 LELAPLGVRVCAVAPGRVDTPMLR--QY-EALGLWEHIRKEQMRQEFTQPN--------- 216 Query: 236 TEVADFVCYLLSERASYMTGVTTNIAGG 263 E+AD V +L+S+ A+ + G T N + G Sbjct: 217 -EIADVVAFLVSDEANCINGCTVNASDG 243 Lambda K H 0.315 0.132 0.378 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: 137 Number of extensions: 7 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: 267 Length of database: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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: 42 (22.0 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