Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate Pf1N1B4_4203 Putative siderophore biosynthesis protein, related to 2-demethylmenaquinone methyltransferase
Query= SwissProt::A5W059 (238 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4203 Length = 238 Score = 366 bits (939), Expect = e-106 Identities = 178/236 (75%), Positives = 206/236 (87%) Query: 1 MNTLIGKTGIVVRNIQRAELDSIDALGRLGVATVHEAQNRKGLLSSKMRPIQQGTSLAGS 60 MN LIGKTG+VVRNIQRAE +D L R GVAT+HEAQ RKGL ++ +RPIQQGT ++GS Sbjct: 1 MNELIGKTGVVVRNIQRAEAALVDELKRFGVATIHEAQGRKGLFATSIRPIQQGTVISGS 60 Query: 61 AVTVLVAPGDNWMFHVAVEQCRPGDVLVVSPSSPCTDGYFGDLLATSLQARGVRALIVDA 120 AVTVLVAPGDNWMFHVAVEQCRPGD+LVV+PSSPC DGYFGDLLATSL+A GVRAL++DA Sbjct: 61 AVTVLVAPGDNWMFHVAVEQCRPGDILVVAPSSPCIDGYFGDLLATSLKAHGVRALVIDA 120 Query: 121 GVRDTQTLRDMGFAVWARAINAQGTVKETLGSVNLPVICGGQLINPGDIVVADDDGVVVV 180 GVRDT TLR+MGF VW+RAI+AQGT+KETLGSVNLP++CGGQL++PGD+VVADDDGVVVV Sbjct: 121 GVRDTHTLREMGFPVWSRAISAQGTIKETLGSVNLPLVCGGQLVHPGDVVVADDDGVVVV 180 Query: 181 RRDECESTLVAAAERAGLEEEKRLRLAAGELGLDIYKMRERLEAKGLRYVDNIEDL 236 RR E + A+ RA LEE+K LRLA GELGLDIY MR RL KGLRYVD++E+L Sbjct: 181 RRTELLQVVEASRARADLEEQKALRLAKGELGLDIYNMRARLAEKGLRYVDSLEEL 236 Lambda K H 0.318 0.136 0.390 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: 242 Number of extensions: 2 Number of successful extensions: 1 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: 238 Length of database: 238 Length adjustment: 23 Effective length of query: 215 Effective length of database: 215 Effective search space: 46225 Effective search space used: 46225 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: 46 (22.3 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