Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate Ac3H11_3411 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= reanno::Koxy:BWI76_RS22230 (259 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3411 Length = 254 Score = 77.4 bits (189), Expect = 3e-19 Identities = 76/231 (32%), Positives = 110/231 (47%), Gaps = 30/231 (12%) Query: 3 QVAVVIGGGQTLGEFLCRGLAAEGYRVAVVDIQSDKATRVAQSINAEYGEGTAWGFGADA 62 Q A+V GG LGE R LAA+G +VAV+D ++ A +VA IN G A D Sbjct: 6 QAALVTGGASGLGEATARALAAQGAKVAVLDRNAELAEKVAADIN-----GIA--CPCDI 58 Query: 63 TSEASVVALARGVDDIFSRVDLLVYSAGIAKAAFI-----SDFALGDFDRSLQVNLVGYF 117 T ASV A +L+ AGI A + S L DF R + +NL+G + Sbjct: 59 TDPASVQAAIDKAAAAHGPARILMNVAGIGSAKRVVQRDGSAAPLEDFVRVVNINLIGTY 118 Query: 118 LCAREF----SRLMIRD-GIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDL 172 +R F S+L + D G +G ++ S + G YSA+K G G+T +A DL Sbjct: 119 NVSRLFAAACSKLDVLDNGERGVMMFTASVAAFDGQVGQQAYSASKAGLAGMTLPMARDL 178 Query: 173 AEYGITVHSLMLGNLLKSPMFQSL-----------LPQYATKLGIPEEQVE 212 A++ I V ++ G L +P+ + L +P + +LG PEE E Sbjct: 179 AQHAIRVCTVAPG-LFATPLMKELPEAVQQSLAASIP-FPPRLGKPEEFAE 227 Lambda K H 0.320 0.137 0.392 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: 151 Number of extensions: 14 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: 259 Length of database: 254 Length adjustment: 24 Effective length of query: 235 Effective length of database: 230 Effective search space: 54050 Effective search space used: 54050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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