Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_046009954.1 OLEAN_RS15340 3-oxoacyl-ACP reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_000967895.1:WP_046009954.1 Length = 256 Score = 108 bits (271), Expect = 9e-29 Identities = 85/266 (31%), Positives = 128/266 (48%), Gaps = 22/266 (8%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGG-------DKHQSSGNYNFWPTD 59 ++ K+ VTGG SGIG A L +GA + ++D+ G + G FW D Sbjct: 4 VENKVAVVTGGISGIGRATSVLLAQEGAKIAVVDLSEGGAQDLINEIESFGGVAKFWQLD 63 Query: 60 ISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNIN 119 + +V + ++ FG+ID LVNNAG+ P+ +E+ E ++ ++NIN Sbjct: 64 TTQEQDVSRVFAEVVDEFGQIDVLVNNAGI------AGVNKPT--HEIAEDEWDSVMNIN 115 Query: 120 QKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179 KGVFL S+ V M+K G I+N+SS GL G+ Y A K A+ +++ + Sbjct: 116 VKGVFLCSKHVIPYMLKSGGGSIINMSSVYGLIGAGDLPPYHAAKGAVRLMSKNDAILYA 175 Query: 180 KHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVA 239 K IRV V P + TP EALA V+ R+ P+G G ++A Sbjct: 176 KDKIRVNSVHPAY-----IWTP-LVEALAEESAEGVKAFRKQLDA-CHPIGHVGEPNDIA 228 Query: 240 DFVCYLLSERASYMTGVTTNIAGGKT 265 V YL S+ + ++TG I GG T Sbjct: 229 YGVLYLASDESKFVTGSELVIDGGYT 254 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: 170 Number of extensions: 7 Number of successful extensions: 4 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: 256 Length adjustment: 25 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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 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