Align Antizyme inhibitor 2; AzI2; Arginine decarboxylase; ADC; ARGDC; Ornithine decarboxylase-like protein; ODC-like protein; ornithine decarboxylase paralog; ODC-p (characterized)
to candidate GFF369 PGA1_c03800 putative lysine/ornithine decarboxylase
Query= SwissProt::Q96A70 (460 letters) >FitnessBrowser__Phaeo:GFF369 Length = 393 Score = 120 bits (301), Expect = 8e-32 Identities = 76/251 (30%), Positives = 129/251 (51%), Gaps = 3/251 (1%) Query: 43 VADLGAIVRKHFCFLKCLPRVRPFYAVKCNSSPGVLKVLAQLGLGFSCANKAEMELVQHI 102 V D A+ R++ + L R R YAVK N P +L+ L ++G F A++AE+E+ Sbjct: 38 VIDSQAVARQYAALAQGLGRARIHYAVKANPEPQILRRLTRMGANFDAASRAEIEMCLAA 97 Query: 103 GIPASKIICANPCKQIAQIKYAAKHGIQLLSFDNEMELAKVVKSHPSAKMVLCIATDDSH 162 G S+I N K+ A I +A + GI + D EL K+ P A++ + + + + Sbjct: 98 GAKPSQITFGNTIKRPADIAFAHEIGITHFAVDALAELDKLADHAPGARVCIRLLVEATG 157 Query: 163 SLSCLSLKFGVSLKSCRHLLENAKKHHVEVVGVSFHIGSGCPDPQAYAQSIADARLVFEM 222 + LS KFG + L++ A+ + V G+SFH+GS +PQ +A ++ V+ Sbjct: 158 ADWPLSRKFGCTAAMALTLMDRARDLDLCVSGLSFHVGSQTREPQMWADTLDQVAQVWRA 217 Query: 223 GTELGHKMHVLDLGGGFPGTEGAKVRF-EEIASVINSALDLYFPEGCGVDIFAELGRYYV 281 GH++ +L++GGGFP + G +V A + + ++ FP+ +I AE GR V Sbjct: 218 AKTAGHELTLLNIGGGFPASYGTEVMAPNRYAQEVMALVNARFPDAS--EIMAEPGRGLV 275 Query: 282 TSAFTVAVSII 292 A +A ++ Sbjct: 276 AEAGAIAAEVL 286 Lambda K H 0.321 0.137 0.422 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: 392 Number of extensions: 15 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: 460 Length of database: 393 Length adjustment: 32 Effective length of query: 428 Effective length of database: 361 Effective search space: 154508 Effective search space used: 154508 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 (21.9 bits) S2: 51 (24.3 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