Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Pf1N1B4_1271 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1271 Length = 450 Score = 95.5 bits (236), Expect = 2e-24 Identities = 75/234 (32%), Positives = 110/234 (47%), Gaps = 11/234 (4%) Query: 9 LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDI--ADEDSRALEAELAGSPIPPVYKR 66 L G++ ++TG GIGA + AR GAEVI LD+ A D AL A L G I Sbjct: 211 LSGRKALVTGAARGIGASIAETLARDGAEVILLDVPPAKADLEALAARLGGRGIT----- 265 Query: 67 CDLMNLEAIKAVFAEIGD-VDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQA 125 D+ +A + + D +D++++NAG LA++T +WD + VNL T+A Sbjct: 266 LDICAEDAATQLIEHLPDGIDIVIHNAGITRDKTLANMTPEFWDAVLAVNLNAPQVLTKA 325 Query: 126 VAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVV 185 + R G VI SIS G Y +KAG+ G+ +A A L I + V Sbjct: 326 LLDSGTLRDNGRVILLASISGIAGNRGQTNYAASKAGLIGLAQAWAPLLSERGISINAVA 385 Query: 186 PGNVKTKRQEKWYTPEGEAQIVAAQCLKGR-IVPENVAALVLFLASDDASLCTG 238 PG ++T Q + P G + G+ +P++VA V +LA TG Sbjct: 386 PGFIET--QMTAHLPFGVREAGRRMSSLGQGGLPQDVAEAVAWLAQPGTGAFTG 437 Lambda K H 0.319 0.137 0.416 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: 203 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 248 Length of database: 450 Length adjustment: 28 Effective length of query: 220 Effective length of database: 422 Effective search space: 92840 Effective search space used: 92840 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 (21.7 bits) S2: 49 (23.5 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