Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_013554474.1 NITSA_RS07785 diaminopimelate decarboxylase
Query= SwissProt::Q58497 (438 letters) >NCBI__GCF_000186245.1:WP_013554474.1 Length = 447 Score = 182 bits (461), Expect = 2e-50 Identities = 134/430 (31%), Positives = 218/430 (50%), Gaps = 29/430 (6%) Query: 20 IDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLA 79 I G D EL + +G+PL+V S+++I+ Y+R EAF + + ++YK N A Sbjct: 32 IAGVDVRELVQNYGSPLFVFSQQEIEEKYHRLHEAFS----SRYPDVVFGWSYKTNYLNA 87 Query: 80 ITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDS 139 I L KLG A+VVS E A+ + K I+FNG K KE + + +E + ++D Sbjct: 88 ICNLYHKLGSIAEVVSEFEYQKARALGIEGKDIIFNGPYKPKEALKVAVEEGAK-IHIDH 146 Query: 140 ISELILINETAKELGETANVAFRINPNVNPKTHPKISTGL--KKNKFGLDVESGIAMKAI 197 + E+ + E A+ELG VA R+N + TG+ + ++FG + ESG A+ AI Sbjct: 147 LFEINDLEEIARELGVKIPVAIRVN----------MDTGIYPQWSRFGFNYESGEAIDAI 196 Query: 198 KMALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEE-GIEIEDVNLGGGL- 255 + + + G+H HIG+ + D S + +ET K+MD + +E G IE +++GGG Sbjct: 197 ERIHSGGLLELTGLHSHIGTFMLDASAYGKETAKLMDLKHQAEERFGYRIEYIDIGGGFA 256 Query: 256 ------GIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGK 309 G+ D +PT D A I + + +P L LE GR L+ AGYLL Sbjct: 257 SKNRLKGVYQSPDVIVPTPDDYAQQITEAIYTHNKSDTLPRLYLETGRHLIDEAGYLLTT 316 Query: 310 VHHIKETP-VTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEVVSIAGGLCESSDVF 368 V K P K ++DAG+N ++ A + ++ ++ + + E + G LC + D+ Sbjct: 317 VQAYKRFPDGMKGYILDAGVN-LLYTATWYNFNFELDRRYEGLNEPSMLNGPLCMNIDIL 375 Query: 369 GRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSK-KGVFLIRERETYADL 427 + L ++ G V+ I VGAY + + + R RP VL K + V LI+E + + Sbjct: 376 SENIMLPPLDRGTVITIGPVGAYNYTQSMQF-IRYRPAAVLIDKERNVHLIKEPDDLETI 434 Query: 428 IAKDIVPPHL 437 K+ +P +L Sbjct: 435 NYKERIPDYL 444 Lambda K H 0.318 0.138 0.393 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: 481 Number of extensions: 39 Number of successful extensions: 6 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: 438 Length of database: 447 Length adjustment: 32 Effective length of query: 406 Effective length of database: 415 Effective search space: 168490 Effective search space used: 168490 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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