Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate 3607967 Dshi_1375 Ornithine decarboxylase (RefSeq)
Query= SwissProt::B4XMC6 (405 letters) >FitnessBrowser__Dino:3607967 Length = 398 Score = 125 bits (315), Expect = 2e-33 Identities = 112/348 (32%), Positives = 166/348 (47%), Gaps = 26/348 (7%) Query: 36 GRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAF 95 G+ +LI YA+KAN IL LA G D S GEI+ AL AG RI F K Sbjct: 61 GQGTLIHYAMKANPAPEILRALAAEGCGFDAASRGEIELALAAGATAARISFGNTIKRPS 120 Query: 96 EIEQALKLNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYISTGLKEN 155 +I A I ++ EL I A AR+ +R+ P Sbjct: 121 DIAFAHAHGIDLFAADAEAELDKIAAHAPG----ARVFLRVLVGATGADWPL------SR 170 Query: 156 KFGVGEKEALEMFLWAKKSAFL--EPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIAL 213 KFG AL + ++AFL PV + FH+GSQ D + ++A+I + A Sbjct: 171 KFGCAPDTALRLM---DRAAFLGLRPVGLSFHVGSQTRDPGMWSDTLDQMAEIWHAGRAR 227 Query: 214 GIDLRFFDVGGGIGVSYENEETIKLYDYA--QGILNALQGLDLTIICEPGRSIVAESGEL 271 G DL ++GGG Y + ++ YA G L + D T++ EPGR +VAE+G + Sbjct: 228 GHDLNLINIGGGFPAFY-GDPILEAETYAGRVGALVRARFGDATVMAEPGRGLVAEAGMI 286 Query: 272 ITQV-LYEKKAQNK--RFVIVDAGMNDFLRPSLYHAKHAIRVITPSKGREISPCDVVGPV 328 + +V L +K+++ R+V +D G L ++ A + +TP G E PC + GP Sbjct: 287 VAEVLLVSRKSEDDLCRWVYLDIGKFSGLAETMEEAIR-YQFVTPHDGGETGPCIMAGPS 345 Query: 329 CESSDTFL--KDAHLP-ELEPGDKIAIEKVGAYGSSMAS-QYNSRPKL 372 C+S+D + HLP L+ GD+I I+ GAY ++ +S +N P L Sbjct: 346 CDSADVLYEQRPVHLPMALQSGDRILIKATGAYTTTYSSVGFNGFPPL 393 Lambda K H 0.319 0.138 0.389 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: 321 Number of extensions: 13 Number of successful extensions: 4 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: 405 Length of database: 398 Length adjustment: 31 Effective length of query: 374 Effective length of database: 367 Effective search space: 137258 Effective search space used: 137258 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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