Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Caulo:CCNA_01892 Length = 546 Score = 115 bits (287), Expect = 3e-30 Identities = 80/262 (30%), Positives = 128/262 (48%), Gaps = 22/262 (8%) Query: 8 KEKIITVTGGASGIGLAIVDELLAQGANVQMIDIH---GGDKHQSSG-NYNFWPTDISSA 63 + +++ VTGGA GIG A G V + D + ++ S G +++ D+SS Sbjct: 31 QSRVVLVTGGADGIGWAACQRFARAGDQVLVADRNVERARERADSLGPDHHAIAMDVSSE 90 Query: 64 SEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGV 123 +++ + + + + FGR+D LVNNAGV P+ P+ + ++ IN G Sbjct: 91 AQIREGFEQLHREFGRLDVLVNNAGVTDPQ-------PTATLDQTAEEVARLQAINVTGA 143 Query: 124 FLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGI 183 FL ++ R M++Q G I+N++S +GL ++ Y+A+KAA+ S TR+ + E G+ Sbjct: 144 FLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKGV 203 Query: 184 RVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVC 243 RV V PG Y I L + IPLGR G E+A+ Sbjct: 204 RVNAVLPG-----------YTRTQMVQDQIDAGLLDPSIVLSRIPLGRMGEPEEMAEGAF 252 Query: 244 YLLSERASYMTGVTTNIAGGKT 265 +L S+ ASY+ G T + GG T Sbjct: 253 FLASDAASYVVGATLVVDGGYT 274 Score = 96.3 bits (238), Expect = 1e-24 Identities = 84/266 (31%), Positives = 119/266 (44%), Gaps = 37/266 (13%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQMI--DIHG--------GDKHQSSGNYNFWPTD 59 ++ +TGG GIG +VD A G + +I D G GD+H D Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVV------QAD 349 Query: 60 ISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNIN 119 I+ + V R+GR+D L+NNAG D PS E F + ++N Sbjct: 350 ITDVAAVEAAFAQAQARWGRLDVLINNAGA------ADVFKPS--LEQTAQDFTSVYDLN 401 Query: 120 QKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELG 179 G ++A AR M + GVIVN+ S +GL ++ Y A KAA+ +RS + E Sbjct: 402 FSGPLATAKAAARLM--SQGGVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWA 459 Query: 180 KHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVA 239 GIRV VAPG +E + AL +++R P+GR G EVA Sbjct: 460 SAGIRVNTVAPGYIETPAVL------ALKSAGRAQFDKIR-----RRAPIGRLGDPMEVA 508 Query: 240 DFVCYLLSERASYMTGVTTNIAGGKT 265 + +L S ASY+ G T + GG T Sbjct: 509 RTIAFLASPAASYVAGATLTVDGGWT 534 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: 362 Number of extensions: 19 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 267 Length of database: 546 Length adjustment: 30 Effective length of query: 237 Effective length of database: 516 Effective search space: 122292 Effective search space used: 122292 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: 50 (23.9 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