Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_101588987.1 BJEO58_RS08150 3-oxoacyl-ACP reductase FabG
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_900169175.1:WP_101588987.1 Length = 247 Score = 112 bits (280), Expect = 8e-30 Identities = 82/265 (30%), Positives = 140/265 (52%), Gaps = 30/265 (11%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTDISSASEV 66 L+ + +TG A G+GLAI + +A+GANV + D++ +++ I A V Sbjct: 4 LEGRTAVITGAAQGLGLAIAEAFVAEGANVVLGDLNEEAVVEAATGLGVGDRAIGMACNV 63 Query: 67 HKT--VDHIIQR----FGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQ 120 + VD + Q+ FG +D +VNNAG+ + ++ E F++++ ++ Sbjct: 64 VELEQVDALAQKAVEVFGSLDIMVNNAGITRDATM---------RKMTEEQFDQVIAVHL 114 Query: 121 KGVFLMSQAVARQMVKQ-RSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179 +G + ++ + M +Q + G I+NVSS SG G GQ+ Y+A KA + T++ +KE+G Sbjct: 115 RGTWNGLKSASGIMREQEQGGSIINVSSISGKVGMLGQTNYSAAKAGIVGMTKAAAKEVG 174 Query: 180 KHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVA 239 +RV V PG + KT + A +++ +L E IP+GR+G +EVA Sbjct: 175 FKNVRVNAVQPGFI-KTAM-------TAAMRQDVIDSKLAE------IPMGRAGEASEVA 220 Query: 240 DFVCYLLSERASYMTGVTTNIAGGK 264 V +L S+ +SYM+G IAGG+ Sbjct: 221 SVVVFLASDMSSYMSGTVQEIAGGR 245 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: 158 Number of extensions: 6 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: 247 Length adjustment: 24 Effective length of query: 243 Effective length of database: 223 Effective search space: 54189 Effective search space used: 54189 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