Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate AO353_05445 AO353_05445 ornithine decarboxylase
Query= SwissProt::B4XMC6 (405 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05445 Length = 387 Score = 113 bits (282), Expect = 1e-29 Identities = 111/373 (29%), Positives = 176/373 (47%), Gaps = 27/373 (7%) Query: 12 KTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGE 71 +TPF + D I QA+ + + F+ K + YA+KAN + I+ LL S D SI E Sbjct: 25 ETPFVVIDTAMIAQAYDDLRAGFEFAK--VYYAVKANPAVEIIDLLKEKGSSFDIASIYE 82 Query: 72 IQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKAR 131 + + L G+ P RI + K + +I + + +S +L+ I A + R Sbjct: 83 LDKVLGRGVTPDRISYGNTIKKSKDIRYFYEKGVRLYATDSEADLRNIAKAAPGSKVYVR 142 Query: 132 ISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLL 191 I + D KFG A+++ + A+ L P + FH+GSQ Sbjct: 143 ILTEGSTTADWPL---------SRKFGCQTDMAMDLLILARDLG-LVPYGISFHVGSQQR 192 Query: 192 DLEPIIEASQKVAKIAKSLIAL-GIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQ 250 D+ A KV I + L GI+L+ ++GGG +Y T L YA+ I+ L+ Sbjct: 193 DISVWDAAIAKVKVIFERLKEEDGINLKLINMGGGFPANYITR-TNSLETYAEEIIRFLK 251 Query: 251 ---GLDLT-IICEPGRSIVAESGELITQ-VLYEKKAQN--KRFVIVDAGMNDFLRPSLYH 303 G DL II EPGRS++A +G L+++ VL +K++ +R+V D G L ++ Sbjct: 252 EDFGDDLPEIILEPGRSLIANAGILVSEVVLVARKSRTAVERWVYTDVGKFSGLIETMDE 311 Query: 304 AKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAH--LP-ELEPGDKIAIEKVGAYGS 360 A + T KG E+ + GP C+S+D ++ LP L GD++ GAY + Sbjct: 312 A-IKFPIWTEKKG-EMEEVVIAGPTCDSADIMYENYKYGLPLNLAIGDRLYWLSTGAYTT 369 Query: 361 S-MASQYNSRPKL 372 S A ++N P L Sbjct: 370 SYSAVEFNGFPPL 382 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: 318 Number of extensions: 14 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: 387 Length adjustment: 31 Effective length of query: 374 Effective length of database: 356 Effective search space: 133144 Effective search space used: 133144 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 Aug 03 2021. The underlying query database was built on Aug 03 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