Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 202371 SO3263 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
Query= metacyc::MONOMER-16231 (254 letters) >FitnessBrowser__MR1:202371 Length = 255 Score = 128 bits (321), Expect = 1e-34 Identities = 82/245 (33%), Positives = 123/245 (50%), Gaps = 6/245 (2%) Query: 7 KTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKGDVA 66 K VL+TG S GIG A A+ G VAI Y + A S LG + A D + Sbjct: 14 KLVLITGGSRGIGAGIAKAFAEAGYWVAITYLNHQDKAVSLA---NILGDKVAAFALDQS 70 Query: 67 DPQTAQDFVAKAVETFGK-VDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMVQA 125 P++ + + + + F + +DV+++N I F D+ D NL G + + QA Sbjct: 71 KPESIKQCITEVEKYFNRSIDVLINNGAIAQEKPFSDITADDFTTMLNTNLRGPFLLAQA 130 Query: 126 AAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCNSV 185 M + G G I+ + SI GG Q HY KAG+ +L QS A + GIR N++ Sbjct: 131 CIPAMQQHGFG-RIINIGSIGGQWGGYNQVHYAAAKAGLINLSQSIAKIYSRDGIRTNTI 189 Query: 186 LPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAALLV 245 G + TE+ + +L + ++ A P+GRLG ED+A +FLAS + Y++G L Sbjct: 190 AIGLVATEMTEHELTTEAGKQ-KAAAIPVGRLGKVEDIASIALFLASQDSDYLSGQTLNA 248 Query: 246 DGGMY 250 +GGMY Sbjct: 249 NGGMY 253 Lambda K H 0.318 0.133 0.379 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: 135 Number of extensions: 6 Number of successful extensions: 3 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: 254 Length of database: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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: 41 (21.7 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