Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate SMc02983 SMc02983 ornithine, DAP, or arginine decarboxylase
Query= SwissProt::Q5HG20 (421 letters) >FitnessBrowser__Smeli:SMc02983 Length = 379 Score = 130 bits (327), Expect = 7e-35 Identities = 111/362 (30%), Positives = 179/362 (49%), Gaps = 32/362 (8%) Query: 28 PTIVYDELQIREQMRRYHRAFKDSGLKYNISYASKAFTCIQMVKLVAEEDLQLDVVSEGE 87 P +V D +R+ + + A DS I YA KA ++++L+A D S E Sbjct: 20 PCLVVDLDVVRDNFKAFRHALPDSA----IYYAVKANPAPEILRLLAGLGSNFDCASVAE 75 Query: 88 LYTALEAGFEPSRIHFHGNNKTKHEIRYALENNIGYFVIDSLEEIELIDRYANDTVQVVL 147 + AL+AG P+RI + K + ++ A I F +DS EE+E I R A Sbjct: 76 IEMALDAGATPNRISYGNTIKKERDVARAHALGISLFAVDSHEEVEKIARAA-------- 127 Query: 148 RVNPGVEAHTHEFIQTGQEDSKFGLSIQYG-LAKKAIDKVQQSKHLKL--KGVHCHIGSQ 204 PG + T E +++ LS ++G + + A+D + + L L GV H+GSQ Sbjct: 128 ---PGARVFCR--VLTDGEGAEWPLSRKFGCVPQMAVDVLVYAHQLGLVSYGVSFHVGSQ 182 Query: 205 ---IEGTEAFIETAKIVLRWLKEQGIQVELLNLGGGFGIKYVEGDESFPIESGIKDITDA 261 ++ +A + AK V L +QGI+++++N+GGGF KY+ S E+ + I A Sbjct: 183 MTKLDAWDAALADAKRVFVQLAKQGIELKMVNMGGGFPTKYLRDVPS--AEAYGQAIFGA 240 Query: 262 IKSEIKVLGIDAPEIGIEPGRSIVGEAGVTLYEVGTI--KEIPEINKYVSIDGGMSDHIR 319 +K K G + PE IEPGR +VG AGV EV + K + +++V +D G + Sbjct: 241 LK---KHFGNNIPETIIEPGRGMVGNAGVIKAEVVLVSKKSDNDSHRWVFLDIGKFGGLA 297 Query: 320 TALYDAKYQALLVNRNEEADDSVTIAGKLCESGDIIIKD--AKLPSSVKRGDYLAILSTG 377 + +A + R+ +A + +AG C+S D++ + LP S+ GD + I TG Sbjct: 298 ETMDEAIRYPIRTARDADAMEPCVLAGPTCDSADVLYEKNMYPLPISLTIGDEVLIEGTG 357 Query: 378 AY 379 AY Sbjct: 358 AY 359 Lambda K H 0.316 0.136 0.378 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: 357 Number of extensions: 15 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: 421 Length of database: 379 Length adjustment: 31 Effective length of query: 390 Effective length of database: 348 Effective search space: 135720 Effective search space used: 135720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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