Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_010632401.1 RH97_RS10960 SDR family oxidoreductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_000246965.1:WP_010632401.1 Length = 271 Score = 318 bits (816), Expect = 6e-92 Identities = 166/271 (61%), Positives = 199/271 (73%), Gaps = 4/271 (1%) Query: 1 MNTWLNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQ----SSGNYNFW 56 M+ WL L + + VTGG+SGIG A+V LL ANV + D+ D S G F Sbjct: 1 MSNWLGLDHQTVIVTGGSSGIGRAVVQTLLENQANVVVADLQEPDHETYEKGSEGQLLFV 60 Query: 57 PTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMV 116 T+++S V V ++ FG+++ LVNNAG+N PRLLVD K P G +EL++ +KM+ Sbjct: 61 KTNVASRESVENLVGQAVKNFGKVNVLVNNAGINLPRLLVDAKEPGGHFELSDDVLDKMI 120 Query: 117 NINQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSK 176 +INQKGVFL SQ R+MVK + GVIVN+ SESGLEGSEGQS YAATKAAL SFTRSW+K Sbjct: 121 SINQKGVFLCSQIAGREMVKAQKGVIVNMVSESGLEGSEGQSGYAATKAALYSFTRSWAK 180 Query: 177 ELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLT 236 ELGK IRVVGVAPGILEKTGLRTP YEEALA+TR ITVEQLR+GY+ SIPL R G+L Sbjct: 181 ELGKFNIRVVGVAPGILEKTGLRTPAYEEALAYTRGITVEQLRKGYTNKSIPLRRDGKLK 240 Query: 237 EVADFVCYLLSERASYMTGVTTNIAGGKTRG 267 EVAD V YL S+RASY+TG T NIAGGK+RG Sbjct: 241 EVADLVAYLSSDRASYITGTTYNIAGGKSRG 271 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: 237 Number of extensions: 5 Number of successful extensions: 2 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: 271 Length adjustment: 25 Effective length of query: 242 Effective length of database: 246 Effective search space: 59532 Effective search space used: 59532 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